Table 2.

Estimated mean differences in plasma IGFBP-3 levels associated with IGFBP-3 SNP variants relative to estimated mean IGFBP-3 levels for reference genotypes (italicized) based on linear regression models for premenopausal Caucasian and African American women

IGFBP-3 SNP*IGFBP-3 locationCaucasians
African Americans
LD blockDiplotype group (position)MAF (%)Genotypen§Mean differences or means, ng/mL (95% CI)LD blockDiplotype group (position)MAF (%)Genotypen§Mean differences or means, ng/mL (95% CI)
rs903889Upstream11 (1)22.0GG22−398 (−754 to −42)Outside1 (1)9.4GT, GG97−131 (−318 to 55)
GT131−67 (−240 to 106)
TT2464,572 (4,470-4,674)TT4714,108 (4,031-4,185)
rs924140Upstream146.8TT82581 (352-810)138.9CC95−560 (−761 to −360)
CT210375 (190-560)CT251−276 (−427 to −125)
CC1074,210 (4,059-4,361)TT2224,304 (4,194-4,414)
rs2854744Upstream11 (2)46.3AA79592 (364-819)11 (2)42.2CC107−534 (−728 to −339)
AC204353 (170-536)AC258−258 (−412 to −105)
CC1074,221 (4,073-4,370)AA1954,305 (4,190-4,421)
rs2854746Exon 111 (3)41.7CC65631 (398-864)11 (3)32.1CC52897 (656-1,138)
CG203379 (206-551)CG259458 (318-598)
GG1304,226 (4,091-4,360)GG2563,798 (3,699-3,897)
rs2471551Intron 111 (4)19.4CC17−345 (−745 to 55)11 (4)20.3CC27−465 (−796 to −133)
CG119−119 (−296 to 57)CG173−258 (−412 to −105)
GG2604,583 (4,484-4,682)GG3644,193 (4,106-4,280)
rs9282734Exon 20.4AC3698 (−233 to 1,629)1 (5)3.3AC, CC3624 (−263 to 311)
AA3934,520 (4,439-4,601)AA5324,079 (4,007-4,151)
rs2453837Intron 30GG3974,524 (4,444-4,605)0GG5684,083 (4,012-4,154)
rs6953668Intron 30.6AG5394 (−330 to 1,119)11 (6)5.0AG, AA55−124 (−362 to 115)
GG3944,522 (4,441-4,603)GG5134,094 (4,020-4,169)
rs3110697Intron 311 (5)41.4AA62−425 (−670 to −181)Outside1 (7)36.1AA78−551 (−764 to −338)
AG203−188 (−366 to −10)AG251−365 (−513 to −217)
GG1314,693 (4,554-4,832)GG2384,325 (4,219-4,431)
rs2453840Intron 421 (6)18.3AA12−535 (−1,008 to −62)22 (1)9.2AC, AA98209 (24-394)
AC121−45 (−221 to 131)
CC2634,560 (4,461-4,658)CC4704,045 (3,969-4,122)
rs2453839Intron 4220.1CC14−325 (−760 to 111)22 (2)40.9CC93−167 (−380 to 45)
CT131−114 (−285 to 57)CT279−28 (−186 to 129)
TT2504,574 (4,474-4,675)TT1944,130 (4,009-4,251)
rs6670Exon 5; 3′ untranslatedOutside2 (1)21.2AA1274 (−402 to 551)33 (1)12.6AT, AA133−44 (−210 to 121)
AT14579 (−90 to 249)
TT2404,494 (4,390-4,598)TT4344,100 (4,020-4,180)
rs13223993DownstreamOutside2 (2)21.4AA1939 (−343 to 421)33 (2)43.6AA116−17 (−216 to 182)
AG13142 (−131 to 216)AG264−147 (−308 to 14)
GG2444,522 (4,419-4,624)GG1844,163 (4,039-4,286)
rs2270628Downstream32 (3)21.0TT15−316 (−743 to 112)43 (3)36.2TT8384 (−131 to 300)
CT137−15 (−186 to 156)CT247−64 (−218 to 90)
CC2474,544 (4,441-4,646)CC2364,101 (3,991-4,211)
rs12671457Downstream32 (4)16.5AC, CC118−119 (−296 to 59)43 (4)5.1AC, CC55−218 (−456 to 21)
AA2674,558 (4,460-4,657)AA5104,106 (4,032-4,181)
  • * Represent tag SNPs except for 3 SNPs that were selected a priori: rs2854744 (-202 A/C), rs2854746 (Ala32Gly), and rs9282734 (His158Pro).

  • LD blocks consist of SNPs with MAF ≥ 5% in strong LD (95% of pairwise SNP comparisons with one-sided 95% CIs for D′ within 0.70-0.98). Group refers to SNP combination for diplotype estimation; position refers to SNP order in each group. SNPs were excluded from diplotype estimation based on the Tagger algorithm (r2 ≥ 0.8) or MAF < 5% for tag SNPs or MAF < 3% for SNPs selected a priori.

  • Based on total n = 402 (Caucasians) and total n = 582 (African Americans).

  • § Caucasians: n = 401, excluded 1 missing plasma IGFBP-3. African Americans: n = 574, excluded 8 missing plasma IGFBP-3.

  • Mean plasma IGFBP-3 levels for reference genotypes estimated from linear regression intercepts are italicized in the last row for each SNP. Mean differences in plasma IGFBP-3 levels for heterozygous and homozygous variants relative to reference genotypes were estimated from β values in linear regression models.