Variant report

Variant	rs7628839
Chromosome Location	chr3:53765448-53765449
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	chr3:53764321..53765834-chr3:53878970..53881230,2	MCF-7	breast:
2	chr3:53764419..53766196-chr3:53767205..53769405,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1020822	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10510765	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11130380	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11705918	0.87[CEU][hapmap]
rs11708227	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11708934	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709505	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11719179	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13075639	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs13076366	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs13092344	0.86[EUR][1000 genomes]
rs17053382	0.81[ASN][1000 genomes]
rs17053417	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2029331	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070616	0.88[ASN][1000 genomes]
rs2125876	0.86[EUR][1000 genomes]
rs2248381	0.80[ASN][1000 genomes]
rs2306865	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2306866	0.86[ASN][1000 genomes]
rs2359204	0.86[EUR][1000 genomes]
rs2633723	0.88[ASN][1000 genomes]
rs28675949	0.84[EUR][1000 genomes]
rs35377175	0.86[EUR][1000 genomes]
rs35414202	0.86[EUR][1000 genomes]
rs35657034	0.84[EUR][1000 genomes]
rs3796346	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4453827	0.86[EUR][1000 genomes]
rs62253777	0.88[ASN][1000 genomes]
rs62253778	0.84[ASN][1000 genomes]
rs6800641	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs723540	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs898423	1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007655	chr3:53742148-53767689	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1000280	chr3:53742736-53770588	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
2	chr3:53753600-53766200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:53761600-53766200	Weak transcription	Lung	lung
4	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
5	chr3:53761800-53766000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:53763000-53765600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:53764200-53766000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:53764200-53766000	Enhancers	Brain Germinal Matrix	brain
9	chr3:53764200-53779800	Weak transcription	Liver	Liver
10	chr3:53764400-53767600	Strong transcription	Fetal Intestine Small	intestine
11	chr3:53764600-53765800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:53764600-53765800	Weak transcription	GM12878-XiMat	blood
13	chr3:53764600-53770800	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53764800-53766800	Strong transcription	Fetal Lung	lung
15	chr3:53764800-53767200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:53764800-53768600	Weak transcription	Right Ventricle	heart
17	chr3:53764800-53769400	Weak transcription	Right Atrium	heart
18	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:53765000-53773600	Weak transcription	Fetal Brain Male	brain
20	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
23	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:53765400-53766200	Strong transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:53765400-53774000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain

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