Variant report

Variant	rs12762731
Chromosome Location	chr10:89579646-89579647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89572839..89574816-chr10:89578225..89580021,2	K562	blood:
2	chr10:89578473..89580973-chr10:89716614..89719298,2	K562	blood:
3	chr10:89578407..89580056-chr10:89597133..89599760,2	K562	blood:

Variant related genes	Relation type
ENSG00000138138	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10082347	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1051441	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10887748	0.89[YRI][hapmap]
rs10887749	0.89[YRI][hapmap]
rs10887750	0.88[YRI][hapmap]
rs10887753	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202526	0.89[YRI][hapmap]
rs11202527	0.89[YRI][hapmap]
rs11202536	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11202538	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11202553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11202557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11202563	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202564	0.87[CEU][hapmap]
rs11202565	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202568	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11498630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11812787	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11816798	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11817759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11818430	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12247482	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12253113	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12413371	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12570131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12570639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12571331	0.86[AMR][1000 genomes]
rs12572346	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12572581	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12573160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12573349	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12765184	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12765681	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12768487	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12769214	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12769771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12770433	1.00[EUR][1000 genomes]
rs12770684	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12771188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12771844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12772552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12773536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12775017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12775041	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs12776656	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12778199	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12779667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12779915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12780234	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12780237	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12781171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12782128	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12782235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12782454	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12783598	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1321934	0.89[MEX][hapmap]
rs17096702	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1819162	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1819163	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1853167	0.87[CEU][hapmap]
rs1923260	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1923261	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1923262	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1960047	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1993845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2038554	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2067661	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34325090	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34466534	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34559481	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34878240	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35254974	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35388513	0.86[AMR][1000 genomes]
rs35662941	0.85[AMR][1000 genomes]
rs35814940	0.86[AMR][1000 genomes]
rs3740278	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3816651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4443987	0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4933461	0.89[YRI][hapmap]
rs4934363	0.89[YRI][hapmap]
rs4934364	0.89[YRI][hapmap]
rs4934366	0.89[YRI][hapmap]
rs4934367	0.89[YRI][hapmap]
rs4934369	0.87[AFR][1000 genomes]
rs6586102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66863455	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7068497	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs7073644	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7090088	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7090432	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7096449	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7098653	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7480	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7481	0.86[ASW][hapmap];0.95[CEU][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7898915	0.87[CEU][hapmap]
rs7901767	0.86[AMR][1000 genomes]
rs7904344	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs7905932	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7908203	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7910692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7913763	0.87[AMR][1000 genomes]
rs7920554	0.89[YRI][hapmap]
rs7920778	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7920910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7921017	0.87[YRI][hapmap]
rs7921889	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9651491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9663978	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9664653	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041462	chr10:89518729-89584284	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12762731	LIPJ	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89578800-89582200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:89579000-89579800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr10:89579000-89580000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr10:89579000-89580000	Enhancers	Placenta	Placenta
5	chr10:89579000-89587200	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:89579000-89596800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:89579200-89580200	Enhancers	Hela-S3	cervix
8	chr10:89579200-89589800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:89579600-89580000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:89579600-89580000	Enhancers	HMEC	breast

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