Variant report

Variant	rs10508715
Chromosome Location	chr10:26500658-26500659
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	RAD21	chr10:26500632-26500882	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr10:26500570-26501222	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr10:26500551-26501186	H1-neurons	neurons:	n/a	n/a
4	ZNF143	chr10:26500649-26501134	H1-hESC	embryonic stem cell:	n/a	n/a
5	TBP	chr10:26500578-26501198	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr10:26500566-26501178	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTBP2	chr10:26500479-26501287	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:26499153..26501750-chr10:26505199..26507063,2	K562	blood:

Variant related genes	Relation type
GAD2	TF binding region
ENSG00000136750	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11014993	0.90[CHB][hapmap]
rs11014995	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014996	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11015014	0.80[EUR][1000 genomes]
rs11594057	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs11819063	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12243037	0.91[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1330572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs1330581	0.81[JPT][hapmap]
rs2236417	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839669	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839670	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758446	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781108	0.89[TSI][hapmap]
rs3781113	0.89[TSI][hapmap]
rs4144102	0.89[TSI][hapmap]
rs4749100	0.81[EUR][1000 genomes]
rs4749108	0.89[TSI][hapmap]
rs61839365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6482538	0.80[YRI][hapmap]
rs7071922	0.84[ASN][1000 genomes]
rs7072136	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073982	0.91[JPT][hapmap]
rs7076544	0.80[CEU][hapmap];0.84[CHB][hapmap]
rs8190582	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8190598	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8190647	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8190706	0.86[CEU][hapmap]
rs8190754	0.89[TSI][hapmap]
rs8190809	0.82[CHB][hapmap]
rs994502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10508715	COMMD3	cis	parietal	SCAN
rs10508715	ABI1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26499600-26500800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:26500400-26500800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr10:26500400-26501200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
4	chr10:26500600-26500800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:26500600-26500800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:26500600-26501200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
7	chr10:26500600-26501200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr10:26500600-26501200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr10:26500600-26501200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:26500600-26501200	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr10:26500600-26501400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr10:26500600-26501600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr10:26500600-26501600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
14	chr10:26500600-26501600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr10:26500600-26501800	Bivalent Enhancer	Fetal Brain Male	brain

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