Variant report

Variant	rs7905247
Chromosome Location	chr10:49765301-49765302
allele	A/T
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	POLR2A	chr10:49763949-49765858	U87	brain:	n/a	n/a
2	POLR2A	chr10:49764894-49765858	U87	brain:	n/a	n/a

Variant related genes	Relation type
ARHGAP22	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10491040	0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs10776614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs10776615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs10776616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857592	0.82[CHB][hapmap]
rs10857596	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10857598	0.87[ASN][1000 genomes]
rs11101368	0.82[CHB][hapmap]
rs11101377	0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[ASN][1000 genomes]
rs11101381	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11101382	1.00[CHB][hapmap]
rs11101384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358311	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12358315	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12412164	0.93[ASN][1000 genomes]
rs1345104	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345109	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs1345110	0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs1345111	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs1348633	0.82[ASN][1000 genomes]
rs1445148	0.91[ASN][1000 genomes]
rs1473323	0.83[ASN][1000 genomes]
rs1814469	0.82[ASN][1000 genomes]
rs1838568	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1838569	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1838570	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs1838573	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs1838574	0.82[ASN][1000 genomes]
rs1838579	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900021	0.80[ASN][1000 genomes]
rs1965170	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2077152	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[ASN][1000 genomes]
rs2120910	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4084916	0.87[ASN][1000 genomes]
rs4101278	0.80[ASN][1000 genomes]
rs4450130	0.82[CHB][hapmap]
rs4838418	0.82[ASN][1000 genomes]
rs4838421	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838422	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838617	0.93[ASN][1000 genomes]
rs4838623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058334	0.91[ASN][1000 genomes]
rs56080723	0.80[ASN][1000 genomes]
rs56248718	0.80[ASN][1000 genomes]
rs6537568	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7071095	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7071480	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7072237	0.82[ASN][1000 genomes]
rs7074631	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7085183	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7085335	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs7087729	1.00[CHB][hapmap]
rs7088010	0.91[ASN][1000 genomes]
rs7094216	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7096053	0.85[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs7098068	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7350424	0.91[ASN][1000 genomes]
rs7350439	0.91[ASN][1000 genomes]
rs747533	0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[ASN][1000 genomes]
rs7894707	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7894971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904456	0.91[ASN][1000 genomes]
rs7916108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935271	0.82[CHB][hapmap];0.96[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7905247	FRMPD2	cis	cerebellum	SCAN
rs7905247	FAM49A	trans	lymphoblastoid	seeQTL
rs7905247	MAPK13	trans	lymphoblastoid	seeQTL
rs7905247	FYN	trans	lymphoblastoid	seeQTL
rs7905247	RIN2	trans	lymphoblastoid	seeQTL
rs7905247	A1CF	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
2	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
3	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
4	chr10:49759200-49770400	Weak transcription	NH-A	brain
5	chr10:49760800-49765400	Strong transcription	HSMM	muscle
6	chr10:49760800-49765600	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr10:49760800-49768800	Weak transcription	Ovary	ovary
8	chr10:49761000-49765400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:49761400-49765600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:49761600-49780600	Weak transcription	HUVEC	blood vessel
11	chr10:49761800-49765400	Strong transcription	NHDF-Ad	bronchial
12	chr10:49762000-49765600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr10:49762600-49772600	Weak transcription	Brain Angular Gyrus	brain
14	chr10:49762800-49765400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:49762800-49765600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:49763200-49780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:49763800-49772600	Weak transcription	Brain Substantia Nigra	brain
18	chr10:49764400-49765400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:49764400-49765400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:49764400-49777800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:49764600-49765400	Weak transcription	HMEC	breast
22	chr10:49764600-49765600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr10:49764800-49766400	Weak transcription	Osteobl	bone
24	chr10:49765000-49773400	Weak transcription	NHLF	lung
25	chr10:49765000-49776400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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