Supplemental Table 1. Type 2 Diabetes Risk Variants Examined in Women with PCOS and Controls

Gene / Variant / Chr / ChrPosition (NCBI 36) / Reference / Risk score / Genotype
Call rate / HWE
P-value
ADAMTS9 / rs4607103 / 3 / 64686944 / (1) / T2D / 1.0 / 0.801
rs6795735 / 3 / 64680405 / 0.99 / 0.043
BCL11A / rs243021 / 2 / 60438323 / (1) / T2D / 1.0 / 0.574
CDC123/CAMK1D / rs12779790 / (1) / T2D / 0.85
(failed) / 0.00030
CDKAL1 / rs10440833 / 6 / 20796100 / (2;3) / T2D / 0.99 / 1.000
rs7754840 / 6 / 20769229 / (2;4) / 1 / 0.912
CDKN2A/B / rs10965250 / 9 / 22123284 / (2-4) / 0.99 / 0.280
rs10811661 / 9 / (2-4) / T2D / 1.0 / 0.381
CENTD2 / rs1552224 / 11 / 72110746 / (5) / T2D / 0.99 / 0.546
CHCHD9 / rs13292136 / 9 / 81141948 / (5) / T2D / 1.0 / 0.421
DUSP9 / rs5945326 / 23 / 152553116 / (5) / T2D / 0.99 / 0.807
ENPP1/PC1 / rs1044498 / 6 / 132214061 / (6) / 1.0 / 0.254
FTO / rs11642841 / 16 / 52402988 / (3;4) / 0.99 / 0.367
rs9939609 / 16 / 52378028 / (7) / T2D / 0.97 / 0.691
HHEX/IDE / rs1111875 / 10 / 94452862 / (2-4) / T2D / 1.0 / 0.213
HMGA2 / rs1531343 / 12 / 64461161 / (5) / T2D / 1.0 / 0.087
HNF1A / rs7957197 / 12 / 119945069 / (5) / T2D / 1.0 / 0.182
HNF1B / rs4430796 / 17 / 33172153 / 1.0 / 0.575
rs757210 / 17 / 33170628 / T2D / 0.99 / 0.616
IGF2BP2 / rs1470579 / (2;4) / T2D / failed design / -
IRS1 / rs2943641 / 2 / 226801989 / (8) / T2D / 1.0 / 0.614
rs7578326 / 2 / 226728897 / 0.99 / 0.543
JAZF1 / rs849134 / 7 / 28162747 / 0.99 / 0.135
rs864745 / 7 / 28147081 / (1) / T2D / 0.96 / 0.0021
KCNQ1 / rs2237892 / 11 / 2796327 / (2;4) / T2D / 1.0 / 1.000
rs231362 / 11 / 2648047 / (5) / T2D / 0.99 / 0.636
KCNJ11 / rs5219 / 11 / 17366148 / (9) / 0.99 / 1.000
rs5215 / 11 / 17365206 / (3) / T2D / 1.0 / 0.841
KLF14 / rs972283 / 7 / 130117394 / (5) / T2D / 0.98 / 0.394
MTNR1B / rs1387153 / 11 / 92313476 / 1.0 / 0.578
rs10830963 / 11 / 92348358 / (10;11) / T2D / 1.0 / 0.241
NOTCH2 / rs10923931 / 1 / 120319482 / (1) / T2D / 1.0 / 0.790
PPARG / rs13081389 / 3 / 12264800 / 1.0 / 0.619
rs1801282 / 3 / 12368125 / (2-4;12) / T2D / 1.0 / 1.000
PRC1 / rs8042680 / 15 / 89322341 / (5) / T2D / 1.0 / 0.838
SLC30A8 / rs13266634 / 8 / 118253964 / (2-4) / T2D / 1.0 / 1.000
rs3802177 / 0.34
(failed) / 0.081
TCF7L2 / rs7903146 / 10 / 114748339 / (4;13;14) / T2D / 0.94 / 0.738
rs11196236 / 10 / 114877712 / (15) / 1.0 / 0.505
rs11196229 / 10 / 114856162 / (15) / 1.0 / 0.235
rs12255372 / 10 / 114798892 / 0.98 / 0.740
THADA / rs11899863 / 2 / 43472323 / 1.0 / 0.311
rs7578597 / 2 / 43586327 / (1) / T2D / 0.98 / 0.379
rs6544661 / 2 / 43565429 / 0.99 / 0.153
rs7567607 / 2 / 43491689 / 0.99 / 0.013
rs12478601 / 2 / 43575012 / (16) / 1.0 / 0.156
rs7582497 / 2 / 43492451 / 0.99 / 0.018
rs12468394 / 2 / 43414665 / (16) / 0.99 / 0.851
rs10186921 / 2 / 43498060 / 0.98 / 0.295
rs6544659 / 2 / 43511927 / 1.0 / 0.109
rs6544660 / 2 / 43542000 / 0.99 / 0.091
rs6751622 / 2 / 43569328 / 1.0 / 0.254
rs6746064 / 2 / 43571154 / 0.99 / 0.182
TP53INP1 / rs896854 / 8 / 96029687 / (5) / T2D / 0.99 / 0.573
TSPAN8/LGR5 / rs4760790 / 12 / 69921061 / 1.0 / 0.734
rs7961581 / 12 / 69949369 / (1) / T2D / 0.95 / 0.817
WFS1 / rs10010131 / 4 / (17) / 0.69
(failed) / 1x10-50
(failed)
rs1801214 / 5 / 6353923 / T2D / 0.99 / 0.557
ZBED3 / rs4457053 / 15 / 76460705 / (5) / T2D / 1.0 / 0.394
ZFAND6 / rs11634397 / 8 / 78219277 / (5) / T2D / 1.0 / 1.000

Supplementary Table 2. Characteristics of Women with PCOS and Control Subjects

Parameter / PCOS / Control / P value
Age (yrs) / 28.4±7.0 / 28.9±8.5 / 0.3
BMI / 30.8±8.6 / 23.5±3.8 / 1.7X10-53
Waist Circumference (cm) / 96.1±18.9 / 80.6±10.6 / 2.5X10-36
Hip Circumference (cm) / 108.8±16.9 / 98.4±9.5 / 5.6X10-22
WHR / 0.88±0.08 / 0.82±0.06 / 7.2X10-29
SBP (mmHg) / 114.1±15.8 / 109.5±12.5 / 1.4X10-6
DBP (mmHg) / 71.6±12.2 / 70.0±9.4 / 0.03
Pulse (beats per minute) / 74.7±10.4 / 68.3±9.4 / 8.3X10-20
Testosterone (ng/dL) / 64.0±33.5 / 35.7±17.2 / 3.8X10-33
SHBG (nmol/L) / 41.2±22.1 / 65.8±31.0 / 1.5X10-24
Androstenedione (ng/mL) / 3.6±1.3 / 3.1±1.5 / 0.0001
DHEAS (µg/dL) / 197±103 / 210±107 / 0.2
LH (IU/L) / 26.9±16.7 / 14.9±12.8 / 6.9x10-21
FSH (IU/L) / 10.5±2.9 / 10.6±3.6 / 0.8
LH:FSH / 2.6±1.4 / 1.4±0.9 / 1.1X10-26
FG Score / 12.6±7.6 / 4.1±2.3 / 3.3X10-72
HbA1C (%) / 5.3±0.3 / 5.2±0.3 / 0.0006
Fasting Glucose (mg/dL) / 84.9±9.4 / 80.9±7.3 / 5.1X10-10
Glucose 120 min (mg/dL) / 99.9±28.6 / 85.2±21.9 / 4.3X10-13
Fasting Insulin (µIU/mL) / 10.6±10.3 / 5.2±3.7 / 2.5X10-18
Insulin 120 min (µIU/mL) / 60.1±62.4 / 25.4±17.5 / 2.0X10-20
HOMA-IR / 2.3±2.4 / 1.0±0.7 / 1.6X10-18
Glucose/Insulin / 14.4±10.5 / 20.0±9.8 / 9.8X10-13
Cholesterol (mg/dL) / 183.4±35.3 / 173.9±32.9 / 0.0004
Triglycerides (mg/dL) / 100.6±63.5 / 67.1±27.4 / 1.4X10-17
HDL (mg/dL) / 52.8±16.3 / 61.5±14.2 / 7.4X10-13
LDL (mg/dL) / 111.6±32.3 / 96.1±28.4 / 1.4X10-10
Ovarian Volume (mL) / 15.0±8.0 / 9.2±4.0 / 1.7X10-25
Follicle Number / 13.5±3.8 / 9.4±3.3 / 5.4X10-44

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