Variant report

Variant	rs10908456
Chromosome Location	chr1:155086148-155086149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155083710..155086275-chr1:155144241..155146172,2	K562	blood:
2	chr1:155084271..155086280-chr1:155088992..155090522,2	MCF-7	breast:
3	chr1:155066425..155068289-chr1:155084131..155086403,2	MCF-7	breast:
4	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
5	chr1:155083403..155086848-chr1:155087073..155089537,3	MCF-7	breast:
6	chr1:155083683..155086275-chr1:155144241..155145800,2	K562	blood:

Variant related genes	Relation type
ENSG00000163462	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000143590	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10796938	1.00[ASN][1000 genomes]
rs10796939	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908454	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908455	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264311	0.80[AMR][1000 genomes]
rs11264312	1.00[ASN][1000 genomes]
rs11264313	0.97[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264321	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264322	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264327	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264328	0.93[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11807418	0.80[EUR][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.97[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12137164	0.81[EUR][1000 genomes]
rs12145362	0.81[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1870939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2306124	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	1.00[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4361977	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625273	1.00[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	1.00[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	1.00[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7366138	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7366355	1.00[ASN][1000 genomes]
rs7367207	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7367758	0.97[ASN][1000 genomes]
rs7367897	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs7534162	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs9297	0.85[JPT][hapmap]
rs9330263	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
6	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10908456	SETDB1	cis	parietal	SCAN
rs10908456	SLC39A1	cis	parietal	SCAN
rs10908456	RPRD2	cis	parietal	SCAN
rs10908456	ADAM15	cis	multi-tissue	Pritchard
rs10908456	SMCP	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155078600-155090200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:155078600-155098400	Weak transcription	Right Atrium	heart
3	chr1:155085000-155086200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:155085000-155089400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:155085600-155086400	Enhancers	HepG2	liver
6	chr1:155085600-155088800	Weak transcription	Hela-S3	cervix
7	chr1:155085800-155086400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:155085800-155086400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:155085800-155086400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:155085800-155086400	Enhancers	NHEK	skin
11	chr1:155086000-155086400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:155086000-155086400	Enhancers	Fetal Muscle Leg	muscle
13	chr1:155086000-155086400	Enhancers	HSMMtube	muscle
14	chr1:155086000-155086800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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