Variant report

Variant	rs4667280
Chromosome Location	chr2:190231962-190231963
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190227574..190230494-chr2:190230881..190233590,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10166385	0.82[EUR][1000 genomes]
rs10166420	0.84[ASN][1000 genomes]
rs10167242	0.87[EUR][1000 genomes]
rs10172607	0.82[EUR][1000 genomes]
rs10173224	0.82[EUR][1000 genomes]
rs10175108	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10184895	0.83[EUR][1000 genomes]
rs10188246	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10198663	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10207812	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs10210634	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804029	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931401	0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs10931403	0.82[EUR][1000 genomes]
rs10931405	0.87[EUR][1000 genomes]
rs10931417	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11676905	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11677167	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11678414	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12474942	0.82[EUR][1000 genomes]
rs12613903	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12621657	0.92[EUR][1000 genomes]
rs12622720	0.80[ASN][1000 genomes]
rs12693539	0.89[ASN][1000 genomes]
rs12693540	0.80[ASN][1000 genomes]
rs12994482	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009912	0.84[ASN][1000 genomes]
rs13015207	0.89[ASN][1000 genomes]
rs13018252	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13035381	0.98[ASN][1000 genomes]
rs13408928	0.82[EUR][1000 genomes]
rs13411992	0.82[EUR][1000 genomes]
rs13413518	0.82[EUR][1000 genomes]
rs1356976	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464135	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1474000	0.92[EUR][1000 genomes]
rs1520854	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1520856	0.96[ASN][1000 genomes]
rs1520858	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1520866	0.82[ASN][1000 genomes]
rs1595749	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs16831454	0.85[ASN][1000 genomes]
rs1851104	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1866605	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1898971	0.80[ASN][1000 genomes]
rs1992295	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2304702	0.87[ASN][1000 genomes]
rs2351632	0.82[EUR][1000 genomes]
rs2351635	0.92[EUR][1000 genomes]
rs2351932	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2351934	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2683012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2882805	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4580411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666775	0.85[ASN][1000 genomes]
rs4667270	0.82[EUR][1000 genomes]
rs4667284	0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs6434334	0.87[EUR][1000 genomes]
rs6434337	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6434340	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434342	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6434343	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6704568	0.92[EUR][1000 genomes]
rs6738193	0.89[ASN][1000 genomes]
rs6747222	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6752545	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761868	0.92[EUR][1000 genomes]
rs734859	0.84[ASN][1000 genomes]
rs7420765	0.85[ASN][1000 genomes]
rs7422875	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7425383	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs745742	0.80[ASN][1000 genomes]
rs7556928	0.98[ASN][1000 genomes]
rs7566093	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574281	0.87[EUR][1000 genomes]
rs7574403	0.89[ASN][1000 genomes]
rs7603704	0.82[EUR][1000 genomes]
rs8179541	0.80[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs8179732	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs893407	0.80[ASN][1000 genomes]
rs939158	0.92[EUR][1000 genomes]
rs9677436	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3451292	chr2:190225623-190266276	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190227600-190234800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:190228800-190232200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:190228800-190233400	Weak transcription	NH-A	brain
4	chr2:190228800-190233800	Weak transcription	HSMM	muscle
5	chr2:190228800-190234000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:190228800-190234000	Weak transcription	NHLF	lung
7	chr2:190228800-190234600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:190228800-190234600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:190228800-190234600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:190228800-190234800	Weak transcription	HSMMtube	muscle
11	chr2:190229000-190232200	Weak transcription	A549	lung
12	chr2:190229000-190233000	Weak transcription	Osteobl	bone
13	chr2:190229000-190233200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:190229000-190233200	Weak transcription	HUVEC	blood vessel
15	chr2:190229000-190233600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:190229000-190233600	Weak transcription	NHDF-Ad	bronchial
17	chr2:190229000-190234400	Weak transcription	Hela-S3	cervix
18	chr2:190229000-190234400	Weak transcription	NHEK	skin
19	chr2:190229200-190233400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:190229200-190234600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:190230800-190232400	Enhancers	Primary T cells from cord blood	blood
22	chr2:190231400-190234600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:190231400-190234600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:190231600-190234600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:190231800-190234600	Weak transcription	HMEC	breast

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