Variant report

Variant	rs10515580
Chromosome Location	chr5:146715841-146715842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10039739	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10040325	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10041697	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10041912	0.89[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10042298	0.87[JPT][hapmap]
rs10059609	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10065264	0.83[ASN][1000 genomes]
rs10070932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10077515	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs10079191	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs10079272	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10477336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515581	0.87[JPT][hapmap]
rs10515582	0.81[JPT][hapmap]
rs11741401	0.85[AFR][1000 genomes]
rs11742132	0.85[AFR][1000 genomes]
rs11747533	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11748615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11951154	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11954258	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11954789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11955235	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12055338	0.80[GIH][hapmap];0.89[LWK][hapmap];0.85[AFR][1000 genomes]
rs12332485	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12514269	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12518250	0.87[JPT][hapmap]
rs12520080	0.87[JPT][hapmap]
rs12520436	0.86[JPT][hapmap]
rs12659468	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13170279	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1364371	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1424293	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs17106458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs17106470	0.87[JPT][hapmap]
rs17106482	0.87[JPT][hapmap]
rs17106492	0.87[JPT][hapmap]
rs17106505	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17106575	0.80[JPT][hapmap]
rs17482095	0.90[TSI][hapmap]
rs17547843	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17548011	1.00[GIH][hapmap]
rs1834122	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1895565	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2400294	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2400295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705038	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705163	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705164	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705165	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705166	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57921061	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62377743	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6866098	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6867255	0.95[ASN][1000 genomes]
rs6872292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6884181	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs6891535	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72831382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7707452	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs918797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs918798	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9885145	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[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
rs10515580	POU4F3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146703600-146716400	Weak transcription	Ovary	ovary
2	chr5:146707000-146716400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:146707400-146716400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:146707600-146725600	Weak transcription	Pancreas	Pancrea
5	chr5:146712600-146716000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:146712600-146716200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:146712800-146716200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:146712800-146716400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:146713000-146716600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:146713800-146720800	Weak transcription	Fetal Kidney	kidney
11	chr5:146715200-146716400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:146715400-146716200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:146715600-146716600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:146715800-146716800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:146715800-146717200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr5:146715800-146717400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links