Variant report

Variant	rs12995892
Chromosome Location	chr2:62868760-62868761
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	chr2:62868727..62871605-chr2:62931209..62933790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1014120	0.83[ASN][1000 genomes]
rs10445940	0.83[ASN][1000 genomes]
rs10445944	0.83[ASN][1000 genomes]
rs11125936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676339	0.86[ASN][1000 genomes]
rs11677640	0.83[ASN][1000 genomes]
rs11679278	0.86[ASN][1000 genomes]
rs11679934	0.84[ASN][1000 genomes]
rs11679950	0.84[ASN][1000 genomes]
rs11680946	0.83[ASN][1000 genomes]
rs11681543	0.85[ASN][1000 genomes]
rs11682112	0.83[ASN][1000 genomes]
rs11687746	0.85[ASN][1000 genomes]
rs11689333	0.86[ASN][1000 genomes]
rs11694041	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11694192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11695167	0.83[ASN][1000 genomes]
rs12991462	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12997664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007226	0.82[ASN][1000 genomes]
rs13017927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030853	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963013	0.86[ASN][1000 genomes]
rs1994397	0.83[ASN][1000 genomes]
rs34184400	0.88[ASN][1000 genomes]
rs34541466	0.82[ASN][1000 genomes]
rs34791478	0.88[ASN][1000 genomes]
rs35032881	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35561669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671043	0.83[ASN][1000 genomes]
rs4671044	0.86[ASN][1000 genomes]
rs4671045	0.84[ASN][1000 genomes]
rs4671046	0.84[ASN][1000 genomes]
rs4671047	0.84[ASN][1000 genomes]
rs4671430	0.81[ASN][1000 genomes]
rs4671431	0.85[ASN][1000 genomes]
rs4671435	0.84[ASN][1000 genomes]
rs4671437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671445	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671447	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72807533	0.84[ASN][1000 genomes]
rs72807535	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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr2:62832200-62868800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:62861400-62869000	Weak transcription	Ovary	ovary
3	chr2:62867600-62869400	Enhancers	HepG2	liver
4	chr2:62867800-62869000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:62867800-62869800	Enhancers	Fetal Intestine Large	intestine
6	chr2:62867800-62870400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:62867800-62870600	Enhancers	Fetal Kidney	kidney
8	chr2:62867800-62871200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:62867800-62871400	Enhancers	Liver	Liver
10	chr2:62868000-62869400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:62868000-62869400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:62868200-62869000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:62868200-62869400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:62868400-62869000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr2:62868400-62869400	Enhancers	Adipose Nuclei	Adipose
16	chr2:62868400-62869800	Flanking Active TSS	A549	lung
17	chr2:62868400-62870400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:62868400-62870400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:62868400-62870800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:62868600-62869000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:62868600-62869000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:62868600-62869000	Enhancers	Small Intestine	intestine
23	chr2:62868600-62869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:62868600-62869400	Enhancers	Fetal Intestine Small	intestine
25	chr2:62868600-62869600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:62868600-62869800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:62868600-62870000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:62868600-62870200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr2:62868600-62870400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:62868600-62870600	Enhancers	Fetal Lung	lung
31	chr2:62868600-62871200	Enhancers	Rectal Smooth Muscle	rectum

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