Variant report

Variant	rs750474
Chromosome Location	chr3:53085280-53085281
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10510761	1.00[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs11706035	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11707575	0.93[EUR][1000 genomes]
rs11707780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710292	0.93[EUR][1000 genomes]
rs11710394	1.00[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs11710707	0.87[EUR][1000 genomes]
rs11711773	0.91[EUR][1000 genomes]
rs11712653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.98[EUR][1000 genomes]
rs11713171	0.98[EUR][1000 genomes]
rs11713206	0.87[EUR][1000 genomes]
rs11713290	0.87[EUR][1000 genomes]
rs11713859	0.91[EUR][1000 genomes]
rs11713926	0.85[JPT][hapmap]
rs11714037	0.87[EUR][1000 genomes]
rs11714876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11714902	0.93[EUR][1000 genomes]
rs11715231	0.82[EUR][1000 genomes]
rs11717132	0.87[EUR][1000 genomes]
rs11717619	1.00[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs11717715	0.87[EUR][1000 genomes]
rs11718388	0.98[EUR][1000 genomes]
rs11718538	0.86[EUR][1000 genomes]
rs11718752	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11718834	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11720191	0.87[EUR][1000 genomes]
rs13058817	0.91[EUR][1000 genomes]
rs13069006	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13072395	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13072457	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs13072818	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs13074524	0.87[EUR][1000 genomes]
rs13076033	0.91[CEU][hapmap]
rs13078834	0.87[EUR][1000 genomes]
rs13078971	0.93[EUR][1000 genomes]
rs13084937	0.93[EUR][1000 genomes]
rs13085514	0.93[EUR][1000 genomes]
rs13085544	0.89[EUR][1000 genomes]
rs13088281	0.85[JPT][hapmap]
rs13091844	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13092352	0.86[EUR][1000 genomes]
rs13320044	0.93[EUR][1000 genomes]
rs1346719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1560333	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17052727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336540	0.87[EUR][1000 genomes]
rs2336541	0.87[EUR][1000 genomes]
rs2564926	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2564941	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2581807	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097417	0.95[EUR][1000 genomes]
rs34121720	0.98[EUR][1000 genomes]
rs34238610	0.93[EUR][1000 genomes]
rs34244302	0.93[EUR][1000 genomes]
rs34313969	0.87[EUR][1000 genomes]
rs34340609	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34493168	0.87[EUR][1000 genomes]
rs34754279	0.87[EUR][1000 genomes]
rs34872575	0.87[EUR][1000 genomes]
rs34933390	0.87[EUR][1000 genomes]
rs34943350	0.87[EUR][1000 genomes]
rs34979715	0.93[EUR][1000 genomes]
rs35076015	0.93[EUR][1000 genomes]
rs35163227	0.93[EUR][1000 genomes]
rs35174175	0.93[EUR][1000 genomes]
rs35230793	0.82[EUR][1000 genomes]
rs35378159	0.87[EUR][1000 genomes]
rs35384050	0.87[EUR][1000 genomes]
rs35385050	0.87[EUR][1000 genomes]
rs35507120	0.93[EUR][1000 genomes]
rs35720014	0.87[EUR][1000 genomes]
rs35737577	0.87[EUR][1000 genomes]
rs35849389	0.87[EUR][1000 genomes]
rs36090694	0.87[EUR][1000 genomes]
rs3796352	1.00[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3806692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821872	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4478072	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs58515094	0.87[EUR][1000 genomes]
rs58660500	0.98[EUR][1000 genomes]
rs59583591	0.93[EUR][1000 genomes]
rs60887045	0.87[EUR][1000 genomes]
rs60942590	0.87[EUR][1000 genomes]
rs61172708	0.87[EUR][1000 genomes]
rs6445555	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445556	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445557	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299622	0.82[EUR][1000 genomes]
rs71301804	0.96[EUR][1000 genomes]
rs71301808	0.98[EUR][1000 genomes]
rs71301809	0.93[EUR][1000 genomes]
rs71301811	0.91[EUR][1000 genomes]
rs71301814	0.93[EUR][1000 genomes]
rs71617204	0.93[EUR][1000 genomes]
rs7622420	0.93[EUR][1000 genomes]
rs7625448	0.93[EUR][1000 genomes]
rs7640293	0.93[EUR][1000 genomes]
rs7645611	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs9756317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875573	0.93[EUR][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	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv590347	chr3:53079048-53088815	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs750474	ITIH4	cis	multi-tissue	Pritchard
rs750474	TMEM110	cis	multi-tissue	Pritchard
rs750474	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53081000-53085400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:53081200-53085400	Weak transcription	Brain Anterior Caudate	brain
3	chr3:53081200-53085400	Weak transcription	Pancreas	Pancrea
4	chr3:53081800-53086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:53085200-53085600	Enhancers	Brain Hippocampus Middle	brain
6	chr3:53085200-53085600	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links