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. 2013 May 14;3(5):e256. doi: 10.1038/tp.2013.13

Table 3. Epistasis between two specific LD blocks in (a) SORCS2 and SORCS3, and (b) SORCS1/SORCS2 and SORCS1/SORCS3.

(a)
                SORCS3
 SORCS2
SORCS3 SORCS2 A1 A2 BETA s.e. Pa DIR CHR1 BP1 GENE1 Locationb CHR2 BP2 GENE2 Locationb
rs749304 rs7665496 ac gt −0.2347 0.0731 0.00133 −−−−−−?−−−−??−− 10 106 990 399 SORCS3 Intron 20 4 7 328 734 SORCS2 Intron 1
rs12263804 rs7665496 cc tt −0.2345 0.0731 0.00134 −−−−−−?−−−−??−− 10 106 993 770 SORCS3 Intron 20 4 7 328 734 SORCS2 Intron 1
rs3750261 rs7665496 cc tt −0.2163 0.0723 0.00279 −−−−−−?−−−−??−− 10 107 023 390 SORCS3 UTR-3 4 7 328 734 SORCS2 Intron 1
rs10884126 rs7665496 ac gt 0.2153 0.0724 0.00292 ++++++?++++??++ 10 107 025 028 SORCS3 Near gene-3 4 7 328 734 SORCS2 Intron 1
rs749304 rs6840423 ag gt 0.1592 0.061 0.00903 +−−+++?++++++−+ 10 106 990 399 SORCS3 Intron 20 4 7 329 324 SORCS2 Intron 1
rs12263804 rs6840423 cg tt 0.1584 0.061 0.00936 +−−+++?++++++−+ 10 106 993 770 SORCS3 Intron 20 4 7 329 324 SORCS2 Intron 1
rs749304 rs7684383 ac gt −0.4259 0.125 0.00066 −−−−−+?−−−−??−− 10 106 990 399 SORCS3 Intron 20 4 7 417 241 SORCS2 Intron 2
rs12263804 rs7684383 cc tt −0.4249 0.125 0.00067 −−−−−+?−−−−??−− 10 106 993 770 SORCS3 Intron 20 4 7 417 241 SORCS2 Intron 2
rs10884126 rs7684383 ac gt 0.4128 0.1224 0.00074 +++++−?++++??++ 10 107 025 028 SORCS3 NearGene-3 4 7 417 241 SORCS2 Intron 2
rs3750261 rs7684383 cc tt −0.4121 0.1223 0.00076 −−−−−+?−−−−??−− 10 107 023 390 SORCS3 UTR-3 4 7 417 241 SORCS2 Intron 2
rs12262245 rs7684383 cc gt −0.7045 0.2318 0.00237 −−−−−+?−−−−??+− 10 106 621 704 SORCS3 Intron 2 4 7 417 241 SORCS2 Intron 2
rs7086583 rs7684383 ac ct −0.7032 0.2317 0.00241 −−−−−+?−−−−??+− 10 106 622 009 SORCS3 Intron 2 4 7 417 241 SORCS2 Intron 2
rs3976793 rs7684383 ac gt 0.6954 0.2332 0.00287 ++++−−?++++??−+ 10 106 616 736 SORCS3 Intron 2 4 7 417 241 SORCS2 Intron 2
rs12259189 rs7684383 cc tt −0.6935 0.2333 0.00295 −−−−++?−−−−??+− 10 106 615 387 SORCS3 Intron 2 4 7 417 241 SORCS2 Intron 2
rs6584629 rs7684383 ac gt 0.6881 0.2349 0.00341 ++++−−?++++??−+ 10 106 608 435 SORCS3 Intron 2 4 7 417 241 SORCS2 Intron 2
rs12249460 rs7684383 ac gt 0.9499 0.3247 0.00345 +++++−?+++−??−+ 10 106 605 440 SORCS3 Intron 2 4 7 417 241 SORCS2 Intron 2
rs749304 rs4234804 aa gg 0.4236 0.125 0.00071 +++++−?++++??++ 10 106 990 399 SORCS3 Intron 20 4 7 417 632 SORCS2 Intron 2
rs10884126 rs4234804 aa gg −0.4137 0.1223 0.00072 −−−−−−?−−−−??−− 10 107 025 028 SORCS3 NearGene-3 4 7 417 632 SORCS2 Intron 2
rs12263804 rs4234804 ca tg 0.4225 0.125 0.00072 +++++−?++++??++ 10 106 993 770 SORCS3 Intron 20 4 7 417 632 SORCS2 Intron 2
rs3750261 rs4234804 ca tg 0.413 0.1223 0.00073 ++++++?++++??++ 10 107 023 390 SORCS3 UTR-3 4 7 417 632 SORCS2 Intron 2
rs12262245 rs4234804 ca gg 0.6971 0.2313 0.00258 +++++−?++++??−+ 10 106 621 704 SORCS3 Intron 2 4 7 417 632 SORCS2 Intron 2
rs7086583 rs4234804 aa cg 0.6958 0.2312 0.00262 +++++−?++++??−+ 10 106 622 009 SORCS3 Intron 2 4 7 417 632 SORCS2 Intron 2
rs3976793 rs4234804 aa gg −0.6885 0.2327 0.00309 −−−−++?−−−−??+− 10 106 616 736 SORCS3 Intron 2 4 7 417 632 SORCS2 Intron 2
rs12259189 rs4234804 ca tg 0.6867 0.2328 0.00318 ++++−−?++++??−+ 10 106 615 387 SORCS3 Intron 2 4 7 417 632 SORCS2 Intron 2
rs6584629 rs4234804 aa gg −0.6823 0.2344 0.0036 −−−−++?−−−−??+− 10 106 608 435 SORCS3 Intron 2 4 7 417 632 SORCS2 Intron 2
rs12249460 rs4234804 aa gg −0.9405 0.3241 0.00371 −−−−−+?−−−+??+− 10 106 605 440 SORCS3 Intron 2 4 7 417 632 SORCS2 Intron 2
(b)
                SORCS1
 SORCS3/SORCS2
SNP1 SNP2 A1 A2 BETA s.e. Pa DIR CHR1 BP1 GENE1 Locationb CHR2 BP2 GENE2 Locationb
rs10786998 rs1670036 aa cc 0.4053 0.1506 0.007122 ?+−++++++−+++?+ 10 108 710 127 SORCS1 Intron 2 10 106 807 189 SORCS3 Intron 4
rs10884391 rs1670036 aa cc 0.4048 0.1507 0.007238 ?+−++++++−+++?+ 10 108 709 892 SORCS1 Intron 2 10 106 807 189 SORCS3 Intron 4
rs11193130 rs1670036 ca tc 0.3929 0.1509 0.009219 ?+−++++++−+++?+ 10 108 718 454 SORCS1 Intron 1 10 106 807 189 SORCS3 Intron 4
rs12245675 rs1670036 ca tc −0.3924 0.1512 0.009424 ?−+−−−−+−+−−−?− 10 108 712 233 SORCS1 Intron 2 10 106 807 189 SORCS3 Intron 4
rs17276802 rs1670036 ca tc −0.392 0.1512 0.009515 ?−+−−−−+−+−−−?− 10 108 712 398 SORCS1 Intron 2 10 106 807 189 SORCS3 Intron 4
rs10884389 rs1670036 ca tc −0.3898 0.1509 0.009817 ?−+−−−−−−+−−−?− 10 108 695 777 SORCS1 Intron 2 10 106 807 189 SORCS3 Intron 4
rs11193209 rs2214459 cc tt −0.3988 0.1451 0.005997 +−++−??−+−?+−−− 10 108 890 136 SORCS1 Intron 1 4 7 667 486 SORCS2 Intron 7
rs17121613 rs4689707 gc tt −0.2004 0.0747 0.007332 −−−−−−−++−−++−+ 10 108 563 116 SORCS1 Intron 3 4 7 326 199 SORCS2 Intron 1

Abbreviations: A1, Allele 1; A2, Allele 2; Beta, beta coefficient; CHR, chromosome; DIR, direction of effect; location, single nucleotide polymorphism (SNP) LD, linkage disequilibrium; location; s.e., standard error of beta coefficient; SORCS1, sortilin-related VPS10 domain-containing receptor 1.

a

P-value cutoff for significance after correction for multiple testing: P=0.0001.

b

Exons 1–18 encode the VPS10 domain.