Variant report

Variant	rs2400294
Chromosome Location	chr5:146722166-146722167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10039739	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10040325	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041697	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs10041912	0.89[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10059609	0.93[ASN][1000 genomes]
rs10065264	0.81[ASN][1000 genomes]
rs10070932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077515	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs10079191	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs10079272	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10477336	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10515580	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]
rs11747533	0.93[ASN][1000 genomes]
rs11748615	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.97[ASN][1000 genomes]
rs11951154	1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11954258	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11954789	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs11955235	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12055338	0.80[GIH][hapmap]
rs12332485	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12514269	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12659468	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13170279	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1364371	0.91[CEU][hapmap];1.00[EUR][1000 genomes]
rs1424293	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs17106458	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17106505	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17482095	0.90[TSI][hapmap]
rs17547843	0.91[CEU][hapmap];0.99[EUR][1000 genomes]
rs17548011	1.00[GIH][hapmap]
rs1834122	0.93[ASN][1000 genomes]
rs1895565	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2400295	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805535	0.81[MEX][hapmap]
rs4705038	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705163	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705164	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705165	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705166	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57921061	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62377743	0.99[EUR][1000 genomes]
rs6866098	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs6867255	0.93[ASN][1000 genomes]
rs6872292	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6884181	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6891535	0.91[CEU][hapmap];0.99[EUR][1000 genomes]
rs72831382	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7707452	0.89[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs889829	0.81[YRI][hapmap]
rs918797	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918798	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885145	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.99[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	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
6	esv2763507	chr5:146718961-146727485	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2400294	POU4F3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146707600-146725600	Weak transcription	Pancreas	Pancrea
2	chr5:146719800-146722400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:146721600-146722400	Weak transcription	Fetal Kidney	kidney
4	chr5:146721800-146726600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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