Variant report

Variant	rs2869407
Chromosome Location	chr4:86815505-86815506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10006487	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs10009525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028816	0.92[EUR][1000 genomes]
rs28440876	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28509253	0.92[EUR][1000 genomes]
rs346497	0.90[JPT][hapmap]
rs346500	0.90[JPT][hapmap]
rs35017635	0.92[EUR][1000 genomes]
rs3806763	0.90[EUR][1000 genomes]
rs60376563	0.92[EUR][1000 genomes]
rs62305506	0.92[EUR][1000 genomes]
rs62305507	0.92[EUR][1000 genomes]
rs62305508	0.92[EUR][1000 genomes]
rs62315531	0.92[EUR][1000 genomes]
rs62315532	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62315533	0.92[EUR][1000 genomes]
rs6531878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531881	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs6531883	0.92[EUR][1000 genomes]
rs6531884	0.92[EUR][1000 genomes]
rs6820289	0.92[EUR][1000 genomes]
rs6820395	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs6825260	0.92[EUR][1000 genomes]
rs7670778	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs7693059	0.92[EUR][1000 genomes]
rs7696763	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9790784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879519	chr4:86786204-86871282	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv2753470	chr4:86804078-86844350	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2869407	DSPP	cis	parietal	SCAN
rs2869407	HELQ	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86790800-86835400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:86791200-86844400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:86808200-86846000	Weak transcription	HUVEC	blood vessel
4	chr4:86811200-86822800	Weak transcription	Primary B cells from cord blood	blood
5	chr4:86812200-86825000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:86812200-86831200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:86812400-86831000	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:86814200-86822000	Weak transcription	NHDF-Ad	bronchial
9	chr4:86815400-86815600	Weak transcription	Fetal Heart	heart
10	chr4:86815400-86815800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:86815400-86825400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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