Variant report

Variant	rs11239766
Chromosome Location	chr10:43264591-43264592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43263804..43266604-chr10:43268900..43270663,2	MCF-7	breast:
2	chr10:43263552..43268206-chr10:43276275..43279426,5	MCF-7	breast:
3	chr10:43262874..43266209-chr10:43268342..43271637,4	K562	blood:
4	chr10:43253135..43254665-chr10:43264247..43266986,2	MCF-7	breast:
5	chr10:43261896..43264649-chr10:43275679..43278435,2	MCF-7	breast:
6	chr10:43258843..43262487-chr10:43264254..43267473,3	K562	blood:
7	chr10:43147543..43150157-chr10:43264028..43266927,2	K562	blood:

Variant related genes	Relation type
ENSG00000165733	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1008751	0.82[JPT][hapmap]
rs10466247	0.81[EUR][1000 genomes]
rs10793636	0.83[CEU][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap]
rs10793638	0.83[CEU][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap]
rs10900267	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10900268	0.81[EUR][1000 genomes]
rs11239763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239779	0.81[TSI][hapmap]
rs11239781	0.83[JPT][hapmap]
rs11239784	0.82[JPT][hapmap]
rs11239785	0.83[JPT][hapmap]
rs13376880	0.83[MKK][hapmap]
rs1539294	0.82[JPT][hapmap]
rs1539295	0.83[MKK][hapmap]
rs1575039	0.82[JPT][hapmap]
rs1819721	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2419111	0.83[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs34081555	0.81[EUR][1000 genomes]
rs3758514	0.82[JPT][hapmap]
rs3982199	0.84[TSI][hapmap]
rs4379783	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4948689	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949033	0.86[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs4949035	0.83[JPT][hapmap]
rs574374	0.80[ASN][1000 genomes]
rs624804	0.83[JPT][hapmap]
rs6593491	0.83[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs6593492	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs6593495	0.83[JPT][hapmap]
rs7074877	0.83[JPT][hapmap]
rs7089449	0.83[JPT][hapmap]
rs7091406	0.81[EUR][1000 genomes]
rs7133	0.83[CEU][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap]
rs7895230	0.82[JPT][hapmap]
rs7902356	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7904312	0.83[JPT][hapmap]
rs7908372	0.81[MKK][hapmap]
rs7922559	0.82[JPT][hapmap]
rs9326544	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv895076	chr10:43234432-43326627	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv825349	chr10:43238099-43265011	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11239766	BMS1	cis	parietal	SCAN
rs11239766	MARCH8	cis	cerebellum	SCAN
rs11239766	ALOX5	cis	cerebellum	SCAN
rs11239766	BMS1	cis	cerebellum	SCAN
rs11239766	HSD17B7P2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43263600-43269600	Weak transcription	Right Atrium	heart
2	chr10:43264400-43264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:43264400-43265600	Enhancers	K562	blood

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