Variant report

Variant	rs28649296
Chromosome Location	chr3:61167697-61167698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61167426..61169661-chr3:61171203..61172847,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11711523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712260	0.90[AFR][1000 genomes]
rs11714429	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11714760	0.86[ASN][1000 genomes]
rs13320670	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13323679	0.86[AFR][1000 genomes]
rs28584187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28738855	0.87[ASN][1000 genomes]
rs34253135	0.86[ASN][1000 genomes]
rs62267451	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62267453	0.86[ASN][1000 genomes]
rs62268422	0.86[ASN][1000 genomes]
rs62268813	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815151	0.86[ASN][1000 genomes]
rs9816826	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9845924	0.86[ASN][1000 genomes]
rs9850978	0.86[ASN][1000 genomes]
rs9856186	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1012435	chr3:61136874-61181318	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1014142	chr3:61136874-61184782	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61158800-61172000	Weak transcription	Pancreas	Pancrea
3	chr3:61159600-61172000	Weak transcription	Gastric	stomach
4	chr3:61159800-61168200	Weak transcription	Fetal Heart	heart
5	chr3:61161000-61186000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:61161400-61169400	Weak transcription	Ovary	ovary
7	chr3:61163800-61168800	Weak transcription	Brain Angular Gyrus	brain
8	chr3:61164000-61168600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:61164200-61168200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:61166200-61170200	Weak transcription	Fetal Lung	lung
11	chr3:61166400-61168000	Enhancers	GM12878-XiMat	blood
12	chr3:61166400-61177800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:61167000-61167800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:61167000-61169000	Enhancers	Brain Hippocampus Middle	brain
15	chr3:61167200-61167800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:61167200-61168000	Enhancers	NH-A	brain
17	chr3:61167200-61168200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:61167200-61168400	Enhancers	NHEK	skin
19	chr3:61167200-61168600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:61167400-61168200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:61167400-61168400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:61167400-61168400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:61167400-61172000	Weak transcription	Psoas Muscle	Psoas
24	chr3:61167600-61167800	Enhancers	HMEC	breast
25	chr3:61167600-61168000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:61167600-61168400	Enhancers	HepG2	liver

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