Table 3

 Potential functional SNPs in the LD block around PTPN22*

NCBI dbSNP ID (Celera ref SNP ID)Relative position from rs2476601 (nucleotide)Hetero-zygosity†Genome positionAmino acid substitution‡Potential functional elements altered by SNP
*All the SNPs show conservation by human–mouse protein (for nsSNP) or DNA sequence alignment; †NA, not available in NCBI dbSNP database build 122; ‡for non-synonymous SNP, amino acid substitution is followed by Gonnet score, and protein functional motif (if there is one neighboring the amino acid substitution) shown in the brackets. Gonnet score ranges from +14.2 (highly conserved) to −5.2 (drastic substitution).
rs3761932 (hCV440662)−220 242NAIntron 7 of MAGI-3/NM_152900Ecotropic viral integration site 1 encoded factor Interferon regulatory factor 7 (IRF-7)
Octamer binding factor 1
rs2208673 (hCV16162717)−192 647NAExon 12 of MAGI-3/NM_020965Serum responsive factor
rs1141016 (hCV8701607)−137 606NA3′UTR of PHTF1/NM_006608Ecotropic viral integration site 1 encoded factor Tax/CREB complex
Muscle specific Mt binding site
rs1141015 (hCV8701602)−137 605NA3′UTR of PHTF1/NM_006608Ecotropic viral integration site 1 encoded factor GATA binding factor 3
Muscle specific Mt binding site
rs1141014 (hCV8701601)−128 9710Exon 13 of PHTF1/NM_006608Trp529Leu (Gonnet score −0.7)Multifunctional c-Abl src type tyrosine kinase
rs2295853 (hCV1329357)−123 6760.480Intron 10 of PHTF1/NM_006608 Xenopus homeodomain factor Xvent-2 Octamer binding factor 1
Pancreatic and intestinal lim homeodomain factor
Steroidogenic factor 1
Pbx1/Meis1 heterodimer
Homeobox protein MEIS1 binding site
Special AT rich sequence binding protein 1
Hepatic nuclear factor 1
rs3789597 (hCV1329356)−121 4290.222Intron 7 of PHTF1/NM_006608Ikaros 3, potential regulator of lymphocyte differentiation
Octamer binding factor 1, POU specific domain
rs2273757 (hCV16179758)−96 7870.080Exon 5 of PHTF1/NM_006608Retinoic acid receptor site, member of nuclear receptors
RAR related orphan receptor alpha1 site
MEF3 binding site
rs3789600 (hCV453456)−43 3460.304Intron 3 of FLJ11220/NM_018364Ecotropic viral integration site 1 encoded factor Hepatic nuclear factor 1 Pax-4 homeodomain binding site, together with PAX-6 involved in pancreatic development
rs958007 (hCV8696660)−20 8600.196Intergenic region between FLJ11220 and PTPN22Promyelocytic leukaemia zinc finger (TF with nine Krueppel-like zinc fingers) protein
Cut-like homeodomain protein
Ecotropic viral integration site 1 encoded factor
rs1217413 (hCV1900170)−19 8180.474Intron 21 of PTPN22/NM_015967Pituitary homeobox 1
rs1217418 (hCV8701537)23 6630.500Intron 4 of PTPN22/NM_015967Myocyte enhancer factor GATA binding factor 1
rs11349 (hCV8701513)60 1690Exon 12 of AP4B1/NM_006594Phe724Ile (Gonnet score 1.0)Cdx-2 mammalian caudal related intestinal transcription factor
POU-factor Tst-1/Oct-6
rs1217401 (hCV8701512)61 3830.471Exon 10 of AP4B1/NM_006594Ser480Leu (Gonnet score −2.1, locates in a protein functional motif of chain B, Ap2 clathrin adaptor core)TCF/LEF-1, involved in the Wnt signal transduction pathway
rs3789613 (hCV25619041)65 4670.407Intron 6 of AP4B1/NM_006594Interferon regulatory factor (IRF) related protein (NF-EM5, PIP, LSIRF, ICSAT)
Ecotropic viral integration site 1 encoded factor
Fkh domain factor FKHRL1 (FOXO)
rs12022378 (hCV25619066)70 821NAExon 1 of DCLRE1B/NM_022836Tyr61His (Gonnet score 2.2)TCF11/MafG heterodimers, binding to subclass of AP1 sites cAMP responsive element binding protein
E4BP4, bZIP domain, transcriptional repressor
v-Myb, AMV v-myb
Pax-3 paired domain protein, expressed in embryogenesis, mutations correlate to Waardenburg Syndrome
rs11102699 (hCV31004540)72 045NAIntron 1 of DCLRE1B/NM_022836Fork head related activator-4 (FOXD1) E2F, involved in cell cycle regulation, interacts with Rb p107 protein
Signal transducer and activator of transcription 6 (STAT6)
rs11102700 (hCV31004541)72 054NAExon 2 of DCLRE1B/NM_022836Phe65Ser (Gonnet score −2.8)CCAAT/enhancer binding protein beta
rs11552448 (no Celera ID)72 074NAExon 2 of DCLRE1B/NM_022836Met72Leu (Gonnet score 2.8)Cut-like homeodomain protein
rs3761936 (hCV27478865)72 0940.339Exon 2 of DCLRE1B/NM_022836AhR nuclear translocator homodimers