Variant report

Variant	rs2062780
Chromosome Location	chr6:54800732-54800733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54793235..54795806-chr6:54798273..54802120,4	MCF-7	breast:
2	chr6:54571628..54573912-chr6:54800682..54803427,2	MCF-7	breast:
3	chr6:54763489..54765995-chr6:54799336..54801622,2	MCF-7	breast:
4	chr6:54790477..54792574-chr6:54798805..54800751,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10485135	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10948865	1.00[EUR][1000 genomes]
rs10948871	0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11961881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11964483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1507112	1.00[EUR][1000 genomes]
rs16886234	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886244	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886248	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062781	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4327697	1.00[EUR][1000 genomes]
rs4428489	1.00[EUR][1000 genomes]
rs55644513	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55954156	1.00[EUR][1000 genomes]
rs56991726	1.00[EUR][1000 genomes]
rs57287621	1.00[EUR][1000 genomes]
rs58495896	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60013096	1.00[EUR][1000 genomes]
rs60517516	1.00[EUR][1000 genomes]
rs61632434	1.00[EUR][1000 genomes]
rs6906651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6915116	1.00[EUR][1000 genomes]
rs6933855	1.00[EUR][1000 genomes]
rs73431481	1.00[EUR][1000 genomes]
rs73432338	1.00[EUR][1000 genomes]
rs73432360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73432383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73434410	1.00[EUR][1000 genomes]
rs73446382	1.00[EUR][1000 genomes]
rs73742854	1.00[EUR][1000 genomes]
rs73742861	1.00[EUR][1000 genomes]
rs73742862	1.00[EUR][1000 genomes]
rs73742869	1.00[EUR][1000 genomes]
rs7756856	1.00[EUR][1000 genomes]
rs7772366	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9296772	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464150	1.00[EUR][1000 genomes]
rs9464164	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464165	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464170	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475070	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475071	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475074	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475076	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475086	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54785600-54805000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54789800-54810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:54797000-54811800	Weak transcription	Esophagus	oesophagus
4	chr6:54797600-54804600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:54798000-54804600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:54798800-54804800	Weak transcription	Fetal Intestine Large	intestine
7	chr6:54798800-54815600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:54799400-54801400	Enhancers	HMEC	breast
9	chr6:54799600-54801600	Enhancers	NHEK	skin
10	chr6:54799800-54800800	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr6:54800000-54801200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:54800000-54801400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:54800000-54801600	Enhancers	Hela-S3	cervix
14	chr6:54800200-54801000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:54800400-54800800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:54800400-54800800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr6:54800400-54800800	Enhancers	Stomach Mucosa	stomach
18	chr6:54800400-54800800	Enhancers	A549	lung
19	chr6:54800400-54801000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:54800400-54801200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:54800400-54802200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:54800400-54807600	Weak transcription	Small Intestine	intestine
23	chr6:54800600-54802600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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