Variant report

Variant	rs11250464
Chromosome Location	chr10:1406364-1406365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:1367350..1368940-chr10:1404924..1406543,2	MCF-7	breast:
2	chr10:1401821..1403761-chr10:1404646..1408124,3	MCF-7	breast:
3	chr10:1405933..1409166-chr10:1409590..1411294,4	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10903440	1.00[CHB][hapmap]
rs10903442	1.00[CHB][hapmap]
rs11250463	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11250466	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11250467	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11250468	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11250496	1.00[CHB][hapmap]
rs2387653	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2805521	1.00[CHB][hapmap]
rs2805523	1.00[CHB][hapmap]
rs2820588	1.00[CHB][hapmap]
rs2820590	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs4554799	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4614361	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4880503	1.00[CHB][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs9794144	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv894725	chr10:1110464-1421516	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1041498	chr10:1117200-1760190	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1052682	chr10:1162925-1675641	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1043944	chr10:1168095-1626019	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv540411	chr10:1168095-1626019	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1045618	chr10:1179519-1537451	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1047911	chr10:1182123-1515126	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1046041	chr10:1195214-2189155	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv894732	chr10:1230968-1492512	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1037054	chr10:1232041-1865296	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv540413	chr10:1232041-1865296	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv549769	chr10:1244020-1764966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv549786	chr10:1293100-1904598	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv825210	chr10:1363185-1438593	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv825211	chr10:1363305-1438350	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv527999	chr10:1367514-1464892	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1053447	chr10:1377945-1447070	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv540415	chr10:1377945-1447070	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv894735	chr10:1396155-1459379	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv3389847	chr10:1404177-1406725	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv3361736	chr10:1404302-1407000	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Radiation response	20923822	GWAS catalog

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1403400-1410600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:1404000-1410600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:1404600-1406800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:1404600-1410200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:1404800-1419600	Weak transcription	Right Atrium	heart
6	chr10:1405000-1406600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:1405800-1406400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:1406000-1406800	Enhancers	Esophagus	oesophagus
9	chr10:1406200-1406400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin

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