Variant report

Variant	rs6554071
Chromosome Location	chr4:54065509-54065510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10014030	0.83[AMR][1000 genomes]
rs10027975	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133248	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11721940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11724062	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11725172	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs11942132	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12715997	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13130337	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs13146499	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1383981	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs1842658	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs2412401	0.81[CEU][hapmap]
rs2412403	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412404	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34426398	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4394057	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4588514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864737	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4864749	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs6554074	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554075	0.82[EUR][1000 genomes]
rs6554078	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554091	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs6554093	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs6822933	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs6827392	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7655632	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7672997	0.89[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs7673864	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7683984	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs7687452	0.86[EUR][1000 genomes]
rs900110	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs9990771	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs9991945	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9998376	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54043200-54077000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
3	chr4:54051000-54073000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:54052400-54065800	Weak transcription	Aorta	Aorta
5	chr4:54053000-54093000	Weak transcription	Primary B cells from cord blood	blood
6	chr4:54054600-54072200	Weak transcription	K562	blood
7	chr4:54056600-54076400	Weak transcription	Ovary	ovary
8	chr4:54058200-54079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:54062800-54071200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:54063000-54066200	Enhancers	Fetal Lung	lung
11	chr4:54063400-54065800	Weak transcription	NHLF	lung
12	chr4:54063400-54066400	Enhancers	NHDF-Ad	bronchial
13	chr4:54063400-54071400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:54063400-54079400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:54064000-54071200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:54064200-54071600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:54064400-54066000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:54064400-54066200	Weak transcription	Fetal Stomach	stomach
19	chr4:54064400-54066400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:54064400-54078400	Weak transcription	Small Intestine	intestine
21	chr4:54064400-54106600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:54064800-54066200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:54065200-54065800	Enhancers	Fetal Kidney	kidney

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