Variant report

Variant	rs3846721
Chromosome Location	chr5:112754567-112754568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10428666	1.00[JPT][hapmap]
rs10519343	0.81[MEX][hapmap]
rs10519346	0.81[MEX][hapmap]
rs10900685	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1116547	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11241201	0.92[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11241206	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11241209	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738075	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738215	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740353	0.81[MEX][hapmap]
rs11741916	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11741963	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11743052	0.92[CEU][hapmap]
rs11744606	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11746821	0.81[EUR][1000 genomes]
rs11747924	0.84[JPT][hapmap];0.83[YRI][hapmap]
rs11748465	0.81[MEX][hapmap]
rs11748524	0.81[MEX][hapmap]
rs11748794	0.86[ASW][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap]
rs11750945	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12152879	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12514091	1.00[JPT][hapmap]
rs12516418	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518849	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12519323	0.88[JPT][hapmap];0.92[YRI][hapmap]
rs12519753	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12519818	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12523255	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1443683	1.00[JPT][hapmap]
rs1517209	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1586943	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17135488	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17135515	0.81[MEX][hapmap]
rs17135526	0.81[MEX][hapmap]
rs17135597	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135608	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135616	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17135630	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17135753	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs17135754	0.88[JPT][hapmap]
rs1833678	0.86[ASW][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[YRI][hapmap]
rs1850410	1.00[JPT][hapmap]
rs1997521	0.92[CEU][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs2042222	0.88[JPT][hapmap];0.92[YRI][hapmap]
rs2068923	0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs3846722	0.88[JPT][hapmap];0.88[YRI][hapmap]
rs4705551	0.88[JPT][hapmap];0.92[YRI][hapmap]
rs4705558	0.88[JPT][hapmap];0.84[YRI][hapmap]
rs4705806	0.92[CEU][hapmap]
rs4705807	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705808	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705809	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705814	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4705817	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4705818	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705819	0.88[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4705826	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs59954246	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66502937	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66583752	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66644309	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66728961	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67268709	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67303814	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67764628	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6864369	1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[YRI][hapmap]
rs6864528	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6877524	1.00[JPT][hapmap]
rs6878001	0.86[ASW][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap]
rs6879800	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6883441	0.88[JPT][hapmap];0.96[YRI][hapmap]
rs6884704	1.00[JPT][hapmap]
rs6887565	0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6888602	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs72792179	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73236478	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7707443	0.88[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs7717000	1.00[CEU][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724707	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7724717	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7724936	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7729433	0.88[JPT][hapmap]
rs957777	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs9800316	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv329948	chr5:112754124-112755837	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3846721	YTHDC2	cis	cerebellum	SCAN
rs3846721	YTHDC2	cis	parietal	SCAN
rs3846721	MCC	cis	parietal	SCAN
rs3846721	DCP2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112752000-112758200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:112753600-112761000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links