Variant report

Variant	rs12654963
Chromosome Location	chr5:57019784-57019785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10057804	0.81[ASN][1000 genomes]
rs10077188	0.83[EUR][1000 genomes]
rs10487615	0.81[ASN][1000 genomes]
rs12153068	1.00[EUR][1000 genomes]
rs12189365	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12652479	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12654040	0.81[ASN][1000 genomes]
rs12654351	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12654850	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12655658	1.00[EUR][1000 genomes]
rs12658940	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16887298	0.81[ASN][1000 genomes]
rs4700209	1.00[EUR][1000 genomes]
rs58041565	0.86[ASN][1000 genomes]
rs58245968	0.95[EUR][1000 genomes]
rs58266257	0.81[ASN][1000 genomes]
rs59516621	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59697426	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60219417	0.89[EUR][1000 genomes]
rs61220614	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6862527	0.86[ASN][1000 genomes]
rs6876911	0.89[EUR][1000 genomes]
rs6883451	0.95[EUR][1000 genomes]
rs6883485	0.95[EUR][1000 genomes]
rs73085594	1.00[EUR][1000 genomes]
rs73089817	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089845	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73089868	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089872	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089877	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089897	0.83[EUR][1000 genomes]
rs7702309	0.82[MEX][hapmap]
rs7713500	0.88[CHD][hapmap];1.00[MEX][hapmap]
rs7714714	0.81[ASN][1000 genomes]
rs7717808	0.81[ASN][1000 genomes]
rs7729312	0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7734079	0.81[ASN][1000 genomes]
rs7734787	0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57012800-57020000	Weak transcription	NHEK	skin
2	chr5:57014400-57020000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:57015400-57020200	Weak transcription	NHDF-Ad	bronchial
4	chr5:57016000-57020000	Weak transcription	HSMM	muscle
5	chr5:57016600-57020400	Weak transcription	A549	lung
6	chr5:57016600-57021400	Weak transcription	Aorta	Aorta
7	chr5:57016800-57020200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:57016800-57020600	Weak transcription	NH-A	brain
9	chr5:57017000-57020200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:57017000-57020600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:57017000-57020800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:57017000-57021400	Weak transcription	HSMMtube	muscle
13	chr5:57017200-57020200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:57017400-57020400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:57017400-57020800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:57018400-57020400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:57019600-57020000	Weak transcription	NHLF	lung

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