Variant report

Variant	rs13075639
Chromosome Location	chr3:53747088-53747089
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53747075..53750039-chr3:53753263..53755603,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10510765	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510766	1.00[ASN][1000 genomes]
rs11705918	0.85[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706303	1.00[ASN][1000 genomes]
rs11708227	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708934	0.84[EUR][1000 genomes]
rs11709505	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719179	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076366	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082692	0.85[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092344	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053417	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs17053532	1.00[ASN][1000 genomes]
rs17641133	1.00[ASN][1000 genomes]
rs2029331	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs2118421	1.00[ASN][1000 genomes]
rs2125876	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232333	1.00[ASN][1000 genomes]
rs2359204	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2612012	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs2633726	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28675949	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35377175	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35414202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657034	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453827	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45560831	1.00[ASN][1000 genomes]
rs45616236	1.00[ASN][1000 genomes]
rs4687736	0.86[CEU][hapmap];0.83[AFR][1000 genomes]
rs55974100	1.00[ASN][1000 genomes]
rs56052250	1.00[ASN][1000 genomes]
rs6800641	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs723540	0.86[EUR][1000 genomes]
rs73092085	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628839	0.90[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53737400-53747800	Weak transcription	Fetal Brain Male	brain
2	chr3:53740200-53764400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:53741200-53751400	Weak transcription	Fetal Brain Female	brain
4	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
5	chr3:53744200-53747800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:53744200-53753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:53744200-53764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:53744400-53748200	Weak transcription	Fetal Heart	heart
9	chr3:53744400-53749400	Weak transcription	Right Ventricle	heart
10	chr3:53744400-53749800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:53744400-53756600	Weak transcription	Lung	lung
12	chr3:53744400-53758600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:53744400-53763800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:53744600-53747600	Weak transcription	Spleen	Spleen
15	chr3:53744600-53749600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:53744600-53755000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:53744600-53755000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:53744600-53756400	Weak transcription	Liver	Liver
19	chr3:53744600-53761200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:53745000-53753800	Strong transcription	Fetal Intestine Small	intestine
21	chr3:53745200-53762800	Strong transcription	Fetal Intestine Large	intestine
22	chr3:53745400-53748400	Enhancers	Left Ventricle	heart
23	chr3:53745600-53750200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:53746000-53747200	Enhancers	Right Atrium	heart
25	chr3:53746200-53747200	Enhancers	Ovary	ovary
26	chr3:53746400-53749200	Weak transcription	Fetal Lung	lung
27	chr3:53746800-53747400	Enhancers	Primary B cells from peripheral blood	blood
28	chr3:53746800-53747400	Enhancers	GM12878-XiMat	blood
29	chr3:53746800-53749200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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