Variant report

Variant	rs6827392
Chromosome Location	chr4:54079598-54079599
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10027975	0.83[EUR][1000 genomes]
rs11133248	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11721940	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs11724781	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11942132	0.86[EUR][1000 genomes]
rs12715997	0.83[EUR][1000 genomes]
rs13146499	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17654608	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2412401	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412403	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2412404	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs28640919	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28876828	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34690074	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4394057	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4557334	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4588514	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs4864737	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864742	0.86[ASN][1000 genomes]
rs6554071	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs6554073	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554074	0.86[EUR][1000 genomes]
rs6554075	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554078	0.86[EUR][1000 genomes]
rs6554098	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6820250	0.83[ASN][1000 genomes]
rs6821328	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6822933	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6857744	0.83[ASN][1000 genomes]
rs751266	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7672997	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7673864	0.85[EUR][1000 genomes]
rs7687452	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	esv17516	chr4:54069503-54079714	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
4	esv2421791	chr4:54070961-54080242	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
5	nsv441876	chr4:54070961-54080242	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	nsv514213	chr4:54073451-54079819	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
2	chr4:54053000-54093000	Weak transcription	Primary B cells from cord blood	blood
3	chr4:54058200-54079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:54064400-54106600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:54066200-54080000	Weak transcription	Psoas Muscle	Psoas
6	chr4:54066400-54099000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:54072600-54085000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:54072800-54089000	Weak transcription	NHDF-Ad	bronchial
9	chr4:54076800-54088200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:54077800-54107600	Weak transcription	Lung	lung
11	chr4:54078000-54089600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:54078000-54107200	Weak transcription	Primary T cells from cord blood	blood

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