Variant report

Variant	rs17410455
Chromosome Location	chr4:86815663-86815664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10007847	0.89[EUR][1000 genomes]
rs1016510	0.81[CHB][hapmap]
rs1016511	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516766	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs10516767	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13435741	0.87[EUR][1000 genomes]
rs13435823	0.89[EUR][1000 genomes]
rs1473009	0.81[CHB][hapmap]
rs1510582	0.81[CHB][hapmap]
rs1546491	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546492	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17011143	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17011177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17011196	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17411008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17411091	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1848917	0.81[CHB][hapmap]
rs1961436	1.00[CEU][hapmap]
rs28434164	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28523568	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28538646	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28605002	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28721934	0.89[EUR][1000 genomes]
rs2904082	0.81[CHB][hapmap]
rs6531882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6851522	0.81[CHB][hapmap]
rs723570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72660111	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs893038	0.89[EUR][1000 genomes]
rs893039	0.89[EUR][1000 genomes]
rs9990941	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9997854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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
rs17410455	FAM175A	cis	parietal	SCAN
rs17410455	HNRNPD	cis	cerebellum	SCAN

Chromatin state (count:12 , 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	chr4:86815400-86815800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:86815400-86825400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:86815600-86815800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:86815600-86815800	Enhancers	Fetal Heart	heart

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