Variant report

Variant	rs2165953
Chromosome Location	chr10:4716542-4716543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:4714435..4717243-chr10:4717743..4721337,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231298	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1025921	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444199	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10508286	0.86[JPT][hapmap];0.97[YRI][hapmap];0.90[ASN][1000 genomes]
rs10795195	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10904310	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10904311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10904312	0.88[ASN][1000 genomes]
rs10904313	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10904316	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11252642	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11252646	0.87[ASN][1000 genomes]
rs11252648	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs11252653	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs12782668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[ASN][1000 genomes]
rs1498270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1838239	0.86[YRI][hapmap]
rs2083873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs2088500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs2165955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2173368	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs313428	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs313433	0.93[EUR][1000 genomes]
rs313455	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs313493	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894787	chr10:4385379-4857717	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv1798456	chr10:4689138-4731081	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1817443	chr10:4689138-4731081	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1831014	chr10:4689138-4731081	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1838419	chr10:4689138-4731081	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1805926	chr10:4689842-4720626	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1809203	chr10:4689842-4720626	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1840346	chr10:4689842-4720626	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1842933	chr10:4689842-4720626	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1848476	chr10:4689842-4720626	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4714000-4717800	Weak transcription	NHDF-Ad	bronchial
2	chr10:4714000-4719600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr10:4714000-4719800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:4714000-4720800	Weak transcription	Right Atrium	heart
5	chr10:4714200-4720800	Weak transcription	Left Ventricle	heart
6	chr10:4714600-4719800	Weak transcription	HSMM	muscle
7	chr10:4714600-4719800	Weak transcription	HSMMtube	muscle
8	chr10:4714800-4717000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:4714800-4719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:4714800-4719600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr10:4714800-4719600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:4715200-4720000	Weak transcription	Adipose Nuclei	Adipose
13	chr10:4715400-4717200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:4715400-4718800	Enhancers	HMEC	breast
15	chr10:4715600-4717000	Enhancers	A549	lung
16	chr10:4715600-4718600	Enhancers	NHEK	skin
17	chr10:4715600-4721000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:4716000-4717200	Genic enhancers	HUVEC	blood vessel
19	chr10:4716000-4718600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:4716200-4717800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:4716200-4719000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:4716200-4719400	Weak transcription	Osteobl	bone
23	chr10:4716200-4719600	Weak transcription	NH-A	brain
24	chr10:4716200-4720000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:4716400-4717200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr10:4716400-4726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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