Variant report

Variant	rs624804
Chromosome Location	chr10:43253587-43253588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43253135..43254665-chr10:43264247..43266986,2	MCF-7	breast:
2	chr10:43251549..43254175-chr10:43277144..43279429,2	K562	blood:
3	chr10:43250846..43253793-chr10:43254051..43256963,2	K562	blood:

Variant related genes	Relation type
ENSG00000165733	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1008751	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs10793636	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs10793638	0.94[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs11239763	0.81[JPT][hapmap]
rs11239766	0.83[JPT][hapmap]
rs11239781	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11239784	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11239785	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11239787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1539292	0.81[AMR][1000 genomes]
rs1539294	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1575039	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes]
rs2142985	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs2419111	0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs2473111	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758514	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4379783	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4949033	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4949035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs592970	0.92[ASN][1000 genomes]
rs610866	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6593491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6593492	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6593494	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs6593495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6593499	0.85[CHB][hapmap]
rs7074877	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs7086238	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs7089449	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7133	0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7895230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7904312	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7922559	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9326544	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1036317	chr10:43189367-43253587	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1045347	chr10:43197101-43253587	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1047398	chr10:43202223-43253587	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1044275	chr10:43207270-43253587	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv550694	chr10:43218552-43253587	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	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
17	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
18	nsv8626	chr10:43235537-43263641	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs624804	BMS1	cis	cerebellum	SCAN
rs624804	MARCH8	cis	parietal	SCAN
rs624804	BMS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43251000-43254000	Weak transcription	Right Atrium	heart
2	chr10:43251000-43259600	Weak transcription	Gastric	stomach
3	chr10:43253000-43254000	Weak transcription	Pancreas	Pancrea

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