Variant report

Variant	rs17590508
Chromosome Location	chr5:146618078-146618079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:146617599..146619376-chr5:146621089..146623393,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11747737	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545027	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2400282	1.00[ASN][1000 genomes]
rs36094045	0.93[ASN][1000 genomes]
rs4705026	0.92[CEU][hapmap];0.92[CHB][hapmap]
rs4705027	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs4705028	0.92[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap]
rs4705133	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4705134	0.95[ASN][1000 genomes]
rs4705135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4705136	0.93[ASN][1000 genomes]
rs4705138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4705139	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs57599778	0.94[ASN][1000 genomes]
rs6580455	0.92[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap]
rs7442689	1.00[ASN][1000 genomes]
rs7442692	0.96[ASN][1000 genomes]
rs7701791	0.91[YRI][hapmap]
rs7717260	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs7720349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17590508	PCYOX1L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146615000-146618400	Weak transcription	Esophagus	oesophagus
2	chr5:146615000-146620800	Weak transcription	Psoas Muscle	Psoas
3	chr5:146615000-146621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:146615200-146621400	Weak transcription	Aorta	Aorta
5	chr5:146616200-146619400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:146616400-146619800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:146616400-146628000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:146617800-146618200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:146617800-146618200	Bivalent Enhancer	Pancreatic Islets	Pancreatic Islet
10	chr5:146618000-146618200	Enhancers	Fetal Brain Female	brain
11	chr5:146618000-146619000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links