Variant report

Variant	rs6592961
Chromosome Location	chr7:50572890-50572891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50518383..50520516-chr7:50572098..50575046,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10244632	0.87[CHB][hapmap]
rs10249982	0.86[CHB][hapmap]
rs12535064	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs12538830	0.87[CHB][hapmap];0.87[CHD][hapmap]
rs17152020	0.81[CEU][hapmap];0.91[GIH][hapmap];0.80[EUR][1000 genomes]
rs1817074	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1982406	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs2100280	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs2198144	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3735274	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs3779084	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[EUR][1000 genomes]
rs4490786	0.81[CEU][hapmap];0.91[GIH][hapmap]
rs4585697	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs4947584	0.81[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs58612109	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6592963	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs7808025	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809758	0.93[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.88[MKK][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs880028	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[EUR][1000 genomes]
rs9918702	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50560800-50581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
5	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
6	chr7:50568200-50574400	Enhancers	Fetal Muscle Leg	muscle
7	chr7:50569000-50592800	Weak transcription	HepG2	liver
8	chr7:50570800-50573000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:50570800-50576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:50571000-50573200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:50571000-50573200	Enhancers	HSMM	muscle
12	chr7:50571000-50576000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:50571000-50580200	Weak transcription	Pancreas	Pancrea
14	chr7:50571000-50582400	Weak transcription	Right Atrium	heart
15	chr7:50571200-50573000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:50571200-50576000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr7:50571800-50576200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:50572200-50573000	Enhancers	Lung	lung
19	chr7:50572400-50573000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr7:50572400-50573000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:50572400-50573200	Enhancers	Adipose Nuclei	Adipose
22	chr7:50572400-50574400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:50572400-50577000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr7:50572600-50573000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr7:50572600-50573200	Enhancers	HSMMtube	muscle
26	chr7:50572600-50573800	Enhancers	Fetal Muscle Trunk	muscle
27	chr7:50572600-50574600	Enhancers	Psoas Muscle	Psoas
28	chr7:50572600-50575400	Weak transcription	Fetal Intestine Large	intestine
29	chr7:50572800-50573200	Enhancers	Brain Substantia Nigra	brain
30	chr7:50572800-50574400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:50572800-50574600	Enhancers	Fetal Thymus	thymus

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