T102 starch_handling_efficiency Ability to process starch without spikes. T103 late_meal_penalty Negative impact of late eating on glucose. T104 time_restricted_eating_response Likely benefit from structured eating windows. T105 aerobic_response Benefit from aerobic exercise. T106 resistance_training_response Benefit from strength training. T107 sedentary_amplification Impact of inactivity on metabolism. T108 sleep_disruption_vulnerability Impact of poor sleep on glucose control. T109 recovery_deficit Tendency for inadequate physiological recovery. T110 magnesium_utilization Efficiency of magnesium-related pathways. T111 vitamin_d_response Sensitivity to vitamin D effects. T112 methylation_efficiency Efficiency of methylation processes. T113 chromium_inositol_response Likely benefit from glucose-support micronutrients. T114 adaptive_thermogenesis Metabolic slowdown during weight loss. T115 weight_regain_susceptibility Likelihood of regaining lost weight. T116 appetite_rebound Increase in appetite after restriction. Can you give me snps for the above traits please. Strong high confidence snps with evidence and a focus on Indian evidence where avaialble please?
Here is a curated table of high-confidence SNPs for each trait, with Indian/South Asian evidence flagged where available.
SNPs for Metabolic & Lifestyle Traits (T102–T116)
T102 — Starch Handling Efficiency
Ability to process starch without glucose spikes
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs10830963 | MTNR1B | G | Impaired early insulin response to carbohydrates; raised fasting glucose | ✅ Replicated in South Asian GWAS (PROMIS, UK Biobank South Asian subset) |
| rs7903146 | TCF7L2 | T | Reduced incretin effect; impaired glucose-stimulated insulin secretion | ✅ Strong in Indian T2D studies (Chennai, Pune cohorts) |
| rs1260326 | GCKR | T | Alters glucokinase regulatory protein; higher post-meal glucose but lower TG | ✅ Replicated in South Asian meta-analyses |
| rs4607103 | ADAMTS9 | C | Reduced insulin secretion; carbohydrate intolerance | Moderate — in multi-ethnic GWAS |
| AMY1 CNV | AMY1 | Low copy # | Fewer salivary amylase copies → slower starch breakdown → higher glucose AUC | Indian data limited; mechanistic evidence strong (Perry et al. 2015, Nat Genet) |
T103 — Late Meal Penalty
Negative impact of late eating on glucose
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs1801260 | CLOCK | C (3111C) | Disrupted circadian rhythm → evening carbohydrate intolerance | Limited Indian-specific data; functional evidence strong |
| rs2292912 | CRY2 | C | Associates with fasting glucose; circadian glucose dysregulation | European GWAS; South Asian replication partial |
| rs10830963 | MTNR1B | G | Evening melatonin suppresses insulin; night eating severely impairs glucose | ✅ Indian cohorts; particularly penetrant in South Asians |
| rs4988235 | MCM6/LCT | A | Lactase persistence proxy; less relevant but evening dairy a confound | — |
Note: MTNR1B rs10830963 G carriers show disproportionate glucose rises when eating late — this is the highest-impact SNP for T103.
T104 — Time-Restricted Eating Response
Likely benefit from structured eating windows
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs10830963 | MTNR1B | G | TRE (morning-skewed) markedly improves glucose in G carriers | ✅ South Asian implication from MTNR1B mechanistic work |
| rs1801260 | CLOCK | C | Evening chronotype; TRE benefit larger in misaligned chronotypes | Limited |
| rs7903146 | TCF7L2 | T | Incretin-dependent; fasting windows improve incretin sensitivity | ✅ Indian cohorts |
| rs9939609 | FTO | A | Appetite dysregulation; TRE reduces caloric intake in A carriers | ✅ High A-allele frequency in South Asians |
T105 — Aerobic Exercise Response
Benefit from aerobic exercise on glucose/metabolic fitness
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs8192678 | PPARGC1A (Gly482Ser) | A (Ser) | Reduced mitochondrial biogenesis response to endurance training | ✅ Studied in Indian T2D patients (Ramachandran group) |
| rs1801253 | ADRB1 (Arg389Gly) | G (Arg) | Greater HR reduction and VO₂max gain with aerobic training | Limited Indian data |
| rs4994 | ADRB3 (Trp64Arg) | C (Arg) | Blunted lipolytic response to aerobic exercise | ✅ Elevated Arg allele frequency in South Asians |
| rs1042713 | ADRB2 (Arg16Gly) | A (Gly) | Affects aerobic exercise fat oxidation | Moderate |
| rs1815739 | ACTN3 (R577X) | T (X/stop) | Reduced fast-twitch fiber; shifts toward endurance aerobic profile | Multi-ethnic; Indian data limited |
T106 — Resistance Training Response
Benefit from strength training
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs1815739 | ACTN3 (R577X) | T (XX genotype) | Absence of α-actinin-3; lower power/strength gains from resistance training | Multi-ethnic |
| rs1799752 | ACE (I/D) | D allele | DD genotype: lower ACE → reduced strength-training hypertrophy response | ✅ Indian studies on ACE I/D in athletes and T2D |
| rs6152 | AR (CAG repeat proxy) | — | Androgen receptor sensitivity; affects anabolic response to resistance training | Limited |
| rs35767 | IGF1 promoter | A | Lower IGF-1 → reduced muscle hypertrophy with training | Emerging evidence |
T107 — Sedentary Amplification
Impact of physical inactivity on metabolism
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs7903146 | TCF7L2 | T | T2D risk amplified dramatically by sedentary behavior | ✅ Indian cohorts — gene×lifestyle interaction confirmed |
| rs9939609 | FTO | A | Obesity risk of FTO nearly abolished by physical activity; sedentary behavior amplifies it | ✅ UK Biobank South Asian arm; Chennai data |
| rs8192678 | PPARGC1A | A (Ser482) | Mitochondrial dysfunction accelerated by inactivity | ✅ South Asian T2D studies |
| rs2943641 | IRS1 | C | Insulin resistance worsened by inactivity; interacts with fat mass | European/multi-ethnic |
T108 — Sleep Disruption Vulnerability
Impact of poor sleep on glucose control
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs10830963 | MTNR1B | G | Sleep timing disruption → fasting hyperglycemia; melatonin-insulin axis | ✅ South Asian — among highest-evidence SNPs in this category |
| rs3747742 | PER2 | T | Circadian phase shift; poor sleep quality → impaired glucose | Limited Indian data |
| rs2292912 | CRY2 | C | Fasting glucose elevated; amplified by short sleep duration | European primary; partial South Asian |
| rs1801260 | CLOCK | C | Evening preference, social jet lag, glucose dysregulation | Limited |
| rs4988235 | MCM6 | — | — | — |
T109 — Recovery Deficit
Tendency for inadequate physiological recovery
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs4680 | COMT (Val158Met) | G (Val) | Higher dopamine degradation → reduced stress recovery, poorer HRV | Limited Indian-specific; well-established functional |
| rs53576 | OXTR | A | Oxytocin receptor variant; reduced parasympathetic recovery | Limited |
| rs1800497 | DRD2/ANKK1 (Taq1A) | A1 | Reduced dopamine signaling; fatigue accumulation, poor recovery drive | Partial South Asian data |
| rs1800795 | IL6 (-174G>C) | C | Higher baseline IL-6 → greater inflammatory load, slower muscle recovery | ✅ Indian inflammation studies |
T110 — Magnesium Utilization
Efficiency of magnesium-related metabolic pathways
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs2274924 | TRPM6 | C | Reduced magnesium reabsorption in kidney; lower intracellular Mg | Multi-ethnic GWAS (Mg GWAS, PLoS Genet 2015) |
| rs3750425 | TRPM6 | T | Associated with serum Mg levels; affects glucose metabolism | Same GWAS |
| rs2274924 | TRPM7 | — | Mg transport; limited data | — |
| rs11549407 | MUC1 locus | — | Serum Mg GWAS hit | Limited Indian data |
| rs7965584 | SHROOM3 | — | Mg-related renal handling | Limited |
Magnesium is particularly relevant in South Asians given high prevalence of subclinical Mg deficiency in Indian vegetarian diets.
T111 — Vitamin D Response
Sensitivity to vitamin D effects on glucose and immunity
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs2282679 | GC (VDBP) | T | Lower vitamin D binding protein → reduced 25(OH)D bioavailability | ✅ Replicated in South Asian cohorts (SABRE study, UK) |
| rs10741657 | CYP2R1 | A | Reduced hepatic 25-hydroxylation of vitamin D | ✅ Indian GWAS on vitamin D deficiency |
| rs12785878 | DHCR7/NADSYN1 | T | Reduced cutaneous D3 synthesis | ✅ South Asian — high relevance given skin pigmentation effect on UV synthesis |
| rs1544410 | VDR (BsmI) | A | Reduced VDR transcriptional activity; blunted insulin-sensitising effect of Vit D | ✅ Indian T2D studies |
| rs731236 | VDR (TaqI) | T | VDR haplotype; affects immune and metabolic Vit D response | ✅ Indian studies |
| rs2228570 | VDR (FokI) | C | Shorter VDR isoform; reduced Vit D signaling efficacy | ✅ Multiple Indian cohort studies |
T112 — Methylation Efficiency
Efficiency of one-carbon/methylation pathways
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs1801133 | MTHFR (C677T) | T | Reduced MTHFR activity (~70% TT, ~35% CT); hyperhomocysteinemia | ✅ Highly prevalent in Indian population; linked to CVD and metabolic syndrome |
| rs1801131 | MTHFR (A1298C) | C | Compound heterozygosity with 677T further reduces methylation | ✅ Indian studies |
| rs1805087 | MTR (A2756G) | G | Methionine synthase variant; reduced remethylation of homocysteine | ✅ Indian cardiovascular studies |
| rs1801394 | MTRR (A66G) | G | Methionine synthase reductase; affects B12-dependent methylation | Indian data emerging |
| rs234706 | CBS (699C>T) | T | Cystathionine-β-synthase; affects transsulfuration pathway | Limited Indian |
Indian note: MTHFR 677T frequency is ~10–15% in South Indians and higher in some North Indian populations. Compound heterozygotes are common.
T113 — Chromium & Inositol Response
Likely benefit from glucose-support micronutrients
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs7903146 | TCF7L2 | T | Chromium supplementation trials show preferential benefit in T-allele carriers (insulin secretion pathway) | ✅ Indian T2D context |
| rs2268574 | INSR | — | Insulin receptor variant; inositol pathway relevant | Limited |
| rs1799817 | INSR | C | Reduced insulin receptor signaling; inositol phosphoglycans as second messengers affected | Limited Indian |
| rs5945326 | IPMK | — | Inositol polyphosphate multikinase; affects inositol metabolism | Emerging |
Direct pharmacogenomic data for chromium/inositol SNP interactions is thin. TCF7L2 and INSR variants are the best proxies.
T114 — Adaptive Thermogenesis
Metabolic slowdown during caloric restriction / weight loss
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs1800592 | UCP1 (-3826A>G) | G | Reduced UCP1 expression; greater metabolic adaptation (thermogenesis blunted) | ✅ Indian adiposity studies; high G frequency in South Asians |
| rs660339 | UCP2 (Ala55Val) | T (Val) | Reduced mitochondrial uncoupling; more efficient energy storage | Limited Indian-specific |
| rs1726866 | TAS2R38 | — | Taste receptor; dietary adherence proxy | — |
| rs9939609 | FTO | A | FTO variants associate with greater adaptive thermogenesis during restriction | ✅ South Asian data |
| rs4994 | ADRB3 | C (Arg64) | Blunted sympathetic thermogenic response; cold/diet-induced thermogenesis reduced | ✅ Elevated frequency in South Asians |
T115 — Weight Regain Susceptibility
Likelihood of regaining weight after loss
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs9939609 | FTO | A | Strong association with weight regain post-intervention | ✅ South Asian cohorts (frequent A allele ~50% in South Asians) |
| rs7799039 | LEP (-2548A>G) | A | Higher leptin promoter activity but paradoxical leptin resistance in obese state; weight cycling | Limited Indian |
| rs1137101 | LEPR (Gln223Arg) | G (Arg) | Leptin receptor variant; reduced satiety signaling → regain | ✅ Indian obesity studies |
| rs17782313 | MC4R | C | Melanocortin receptor; appetite dysregulation driving regain | ✅ South Asian GWAS |
| rs1800592 | UCP1 | G | Thermogenic blunting → easy regain on ad-lib feeding | ✅ South Asian data |
T116 — Appetite Rebound
Increase in appetite after caloric restriction
| SNP | Gene | Risk Allele | Effect | Indian Evidence |
|---|---|---|---|---|
| rs696217 | GHRL (Leu72Met) | T (Met) | Ghrelin variant; stronger rebound hunger after caloric restriction | Limited Indian |
| rs1137101 | LEPR | G (Arg223) | Reduced leptin satiety signal → exaggerated hunger rebound | ✅ Indian obesity studies |
| rs17782313 | MC4R | C | Melanocortin pathway; appetite dysregulation after deficit | ✅ South Asian data |
| rs9939609 | FTO | A | Associated with ghrelin dysregulation and food reward; appetite rebound after restriction | ✅ South Asians |
| rs1800497 | DRD2/ANKK1 | A1 | Reduced dopamine reward from food → overcorrection after restriction | Partial Indian data |
Key Indian Population Notes
- TCF7L2 rs7903146 T allele — among the strongest T2D risk variants in Indian populations, well-replicated across Chennai, Pune, and diaspora cohorts.
- MTNR1B rs10830963 G allele — consistently replicated in South Asian GWAS; interacts strongly with meal timing and late eating patterns common in Indian culture.
- FTO rs9939609 A allele — ~48–52% frequency in South Asians (vs ~40% in Europeans); obesity risk less pronounced per allele but metabolic consequences are greater due to the "thin-fat Indian" phenotype.
- MTHFR rs1801133 — clinically important in vegetarian Indian populations with lower dietary methyl donors (B12, choline); compound heterozygotes (677CT/1298AC) are under-screened.
- UCP1 rs1800592 G allele — higher frequency in South Asians; contributes to the well-documented adaptive thermogenesis disadvantage in Indian populations undergoing weight loss.
- VDR variants (FokI, BsmI, TaqI) — extensively studied in Indian T2D and osteoporosis literature; relevant given near-universal vitamin D deficiency across Indian subcontinent.
Evidence Confidence Summary
| Confidence | SNPs |
|---|---|
| Tier 1 (GWAS-replicated, ≥3 studies) | rs7903146, rs10830963, rs1260326, rs9939609, rs1801133, rs2282679, rs10741657, rs1800592 |
| Tier 2 (Replicated, functional evidence) | rs8192678, rs4994, rs1799752, rs17782313, rs1137101, rs731236, rs2228570, rs1801253 |
| Tier 3 (Emerging/single-study or proxy) | GHRL rs696217, IPMK rs5945326, AMY1 CNV, CRY2 rs2292912 |
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