Variant report

Variant	rs9288658
Chromosome Location	chr2:231030179-231030180
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	chr2:231028594..231030818-chr2:231037316..231039671,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135899	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10210254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1060759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1137604	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1137605	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12328528	0.83[ASN][1000 genomes]
rs13026113	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13026121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13026878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2114586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731723	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs3731725	0.83[ASN][1000 genomes]
rs3943889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4283410	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4381771	0.83[ASN][1000 genomes]
rs4624369	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4973278	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973279	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4973281	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973282	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6436917	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs722555	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs7583955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957683	0.95[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231023600-231032200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:231024800-231036400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:231025000-231031400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:231025000-231031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:231025000-231031400	Weak transcription	Adipose Nuclei	Adipose
6	chr2:231025000-231031400	Weak transcription	Fetal Thymus	thymus
7	chr2:231025000-231031400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:231025000-231031600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:231025000-231032000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:231025000-231032000	Weak transcription	Left Ventricle	heart
11	chr2:231025000-231032000	Weak transcription	Ovary	ovary
12	chr2:231025000-231032200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:231025000-231032200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:231025000-231032200	Weak transcription	Lung	lung
15	chr2:231025000-231033800	Weak transcription	Small Intestine	intestine
16	chr2:231025000-231034200	Weak transcription	Brain Substantia Nigra	brain
17	chr2:231025000-231034400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:231025000-231034400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:231025000-231034400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:231025000-231034400	Weak transcription	Pancreas	Pancrea
21	chr2:231025000-231034600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:231025000-231034800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:231025000-231035000	Weak transcription	Placenta	Placenta
24	chr2:231025000-231035400	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:231025000-231036200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:231025000-231036200	Weak transcription	Fetal Intestine Large	intestine
27	chr2:231025000-231036600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:231025000-231036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:231025000-231036600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:231025000-231036600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:231025000-231040000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:231025400-231030800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:231025400-231035000	Weak transcription	Right Ventricle	heart
34	chr2:231025600-231032000	Weak transcription	Spleen	Spleen
35	chr2:231026000-231032200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:231026200-231036200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:231026400-231036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:231026400-231041600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:231026400-231041800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:231026600-231032000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:231026600-231035000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:231026600-231037000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:231026600-231040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:231026600-231041400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:231026800-231030800	Weak transcription	Liver	Liver
46	chr2:231027000-231031400	Weak transcription	Thymus	Thymus
47	chr2:231027800-231032000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:231027800-231032200	Weak transcription	Aorta	Aorta
49	chr2:231028200-231036600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:231028400-231031600	Weak transcription	Stomach Smooth Muscle	stomach

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