Variant report

Variant	rs12284629
Chromosome Location	chr11:85804432-85804433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr11:85804343-85804486	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000238666	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10128700	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10501603	0.88[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs10501605	0.94[CEU][hapmap]
rs10898431	0.88[CEU][hapmap]
rs11234513	0.88[CEU][hapmap]
rs11234517	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs11234544	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11234548	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12270433	0.82[EUR][1000 genomes]
rs12271390	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12276435	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12277986	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12281494	0.91[EUR][1000 genomes]
rs12282655	0.87[EUR][1000 genomes]
rs12292364	0.94[EUR][1000 genomes]
rs12294130	0.88[CEU][hapmap];1.00[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17159904	0.83[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs17745105	0.94[CEU][hapmap]
rs17745153	0.88[CEU][hapmap]
rs17745236	0.86[CEU][hapmap]
rs17745248	0.81[EUR][1000 genomes]
rs17745273	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs17745474	0.94[EUR][1000 genomes]
rs17817690	0.94[CEU][hapmap]
rs17817859	0.94[CEU][hapmap]
rs17817919	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17817956	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2001241	0.87[EUR][1000 genomes]
rs4943937	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4944550	1.00[CEU][hapmap]
rs4944551	0.87[CEU][hapmap]
rs4944552	0.88[CEU][hapmap]
rs4944555	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4944556	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs55791429	0.84[EUR][1000 genomes]
rs55815523	0.81[EUR][1000 genomes]
rs56187740	0.83[EUR][1000 genomes]
rs56207019	0.82[EUR][1000 genomes]
rs7128598	0.82[EUR][1000 genomes]
rs72950443	0.86[EUR][1000 genomes]
rs72950453	0.87[EUR][1000 genomes]
rs72950456	0.87[EUR][1000 genomes]
rs72959906	0.91[EUR][1000 genomes]
rs72959929	0.99[EUR][1000 genomes]
rs72965157	0.82[EUR][1000 genomes]
rs72965166	0.86[EUR][1000 genomes]
rs7927222	0.94[CEU][hapmap];0.86[GIH][hapmap]
rs7943152	1.00[CEU][hapmap];0.91[EUR][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	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12284629	GRM5	cis	cerebellum	SCAN
rs12284629	FAM181B	cis	parietal	SCAN
rs12284629	PICALM	cis	cerebellum	SCAN
rs12284629	CCDC83	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85803400-85810800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:85804000-85804600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:85804400-85806200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:85804400-85811000	Weak transcription	Osteobl	bone

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