Variant report

Variant	rs10474734
Chromosome Location	chr5:2004208-2004209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10035144	0.86[ASN][1000 genomes]
rs10043083	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10045683	0.85[ASN][1000 genomes]
rs1017924	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs10462750	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10474733	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133918	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs1123381	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs1123390	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs1123391	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs11749073	1.00[ASN][1000 genomes]
rs12188545	0.84[ASN][1000 genomes]
rs12521254	0.87[ASN][1000 genomes]
rs12716127	0.86[ASN][1000 genomes]
rs13166888	0.85[ASN][1000 genomes]
rs1486937	0.92[ASN][1000 genomes]
rs1552435	0.84[EUR][1000 genomes]
rs1601641	0.92[ASN][1000 genomes]
rs16902318	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16902321	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2129471	0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2129472	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28392808	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3902820	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4074914	0.81[EUR][1000 genomes]
rs4246752	0.84[ASN][1000 genomes]
rs4246753	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4246754	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4254943	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4314451	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4371796	0.85[ASN][1000 genomes]
rs4398675	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4398680	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4407661	0.84[ASN][1000 genomes]
rs4413568	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs4463207	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4505990	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4526149	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975719	0.85[EUR][1000 genomes]
rs4975777	0.84[ASN][1000 genomes]
rs4975779	0.90[ASN][1000 genomes]
rs4975786	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975794	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4975795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4975796	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs4975797	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4975798	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4975802	0.81[EUR][1000 genomes]
rs57434783	0.86[ASN][1000 genomes]
rs61177713	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67659713	0.82[ASN][1000 genomes]
rs6867032	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7729761	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9312970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965276	0.92[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	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10474734	SLC6A18	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1992000-2007000	Weak transcription	Right Ventricle	heart
2	chr5:2002800-2005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:2003600-2004600	Enhancers	Pancreas	Pancrea
4	chr5:2003800-2007400	Weak transcription	Fetal Heart	heart
5	chr5:2004200-2004600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:2004200-2007800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links