Variant report

Variant	rs4667274
Chromosome Location	chr2:190130511-190130512
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	chr2:190086028..190087990-chr2:190129145..190131338,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10181597	0.84[CHD][hapmap]
rs10187060	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10755004	0.96[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10931400	0.86[EUR][1000 genomes]
rs10931404	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931414	0.84[EUR][1000 genomes]
rs10931415	0.84[EUR][1000 genomes]
rs1112578	0.80[EUR][1000 genomes]
rs1157910	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11681286	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11691604	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12104769	0.85[EUR][1000 genomes]
rs12105389	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12611950	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12615823	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12616234	0.80[EUR][1000 genomes]
rs12618438	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12621035	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12621806	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12621939	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12990235	0.80[EUR][1000 genomes]
rs12991770	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12993719	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995956	0.86[EUR][1000 genomes]
rs12999122	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12999996	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13004187	0.88[EUR][1000 genomes]
rs13004722	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13005652	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13005821	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13011374	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13011485	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13012327	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13012649	0.85[EUR][1000 genomes]
rs13015283	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13016231	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13017413	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13019076	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13021508	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13022633	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13028967	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13029705	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13031211	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13031549	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13032853	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs13033421	0.85[EUR][1000 genomes]
rs1356162	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1356163	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1356164	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1356165	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1356167	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1356168	0.96[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1356977	0.85[EUR][1000 genomes]
rs1399991	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1399992	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1515874	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1515876	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520857	0.96[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs1520859	0.88[EUR][1000 genomes]
rs1520863	0.84[EUR][1000 genomes]
rs1520864	0.80[EUR][1000 genomes]
rs1568334	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1878085	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1949484	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1949604	0.83[EUR][1000 genomes]
rs1949605	0.84[EUR][1000 genomes]
rs1965422	0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2138374	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2222256	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2351627	0.86[EUR][1000 genomes]
rs2351636	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35475196	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35772309	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3914778	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233801	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4353589	0.82[EUR][1000 genomes]
rs4428040	0.85[EUR][1000 genomes]
rs4666774	0.86[EUR][1000 genomes]
rs4667264	0.96[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs4667265	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4667272	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667276	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4667277	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4667281	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4998559	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60124911	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62182416	0.80[EUR][1000 genomes]
rs6434317	0.84[CHD][hapmap]
rs6434318	0.84[CHD][hapmap]
rs6434339	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6708419	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6714088	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6719104	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6737071	0.86[EUR][1000 genomes]
rs7419276	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7419888	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7561002	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7564611	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7576165	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7587147	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587956	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609495	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs963738	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[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	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	nsv1014747	chr2:190097979-190132854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4667274	COL5A2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190123200-190132200	Weak transcription	Pancreas	Pancrea
2	chr2:190126600-190132200	Weak transcription	NH-A	brain
3	chr2:190126600-190132400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:190126800-190132000	Weak transcription	Osteobl	bone
5	chr2:190127000-190132000	Weak transcription	NHLF	lung
6	chr2:190127200-190131800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:190127200-190133200	Weak transcription	Fetal Lung	lung
8	chr2:190130000-190130600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:190130000-190130600	Weak transcription	NHDF-Ad	bronchial
10	chr2:190130200-190132000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:190130200-190132000	Weak transcription	HSMM	muscle
12	chr2:190130400-190130600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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