Variant report

Variant	rs2345049
Chromosome Location	chr4:62637158-62637159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10000772	0.84[EUR][1000 genomes]
rs10006513	0.80[AMR][1000 genomes]
rs10015258	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735887	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12509742	0.85[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs13122879	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1376306	0.80[AMR][1000 genomes]
rs1376307	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs1450901	0.80[AMR][1000 genomes]
rs1470721	0.80[AMR][1000 genomes]
rs17090543	0.81[GIH][hapmap]
rs1817052	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1901223	0.81[CEU][hapmap];0.95[GIH][hapmap];0.80[EUR][1000 genomes]
rs2122640	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2122643	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2167280	0.82[EUR][1000 genomes]
rs2345043	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2345044	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2345045	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2345046	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2345047	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345048	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28735546	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861113	0.81[AMR][1000 genomes]
rs4487384	0.81[EUR][1000 genomes]
rs4493573	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs4860104	0.80[AMR][1000 genomes]
rs4860434	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4860435	0.80[AMR][1000 genomes]
rs6855424	0.81[EUR][1000 genomes]
rs7656882	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs969965	0.80[AMR][1000 genomes]
rs9942184	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv829949	chr4:62615637-62761629	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr4:62635800-62638800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:62635800-62639600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:62636400-62638000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:62636400-62639800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:62636600-62637200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:62636600-62637600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:62636600-62638000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:62636600-62638000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:62636600-62638400	Enhancers	HMEC	breast
10	chr4:62636600-62638600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:62636800-62638000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:62636800-62638400	Enhancers	NHEK	skin
13	chr4:62636800-62639000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr4:62636800-62639600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:62636800-62639600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:62636800-62640800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr4:62637000-62637200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:62637000-62637400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:62637000-62637600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:62637000-62637600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:62637000-62639800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr4:62637000-62640000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:62637000-62641000	Enhancers	HUES6 Cell Line	embryonic stem cell

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