Variant report

Variant	rs9458023
Chromosome Location	chr6:161176256-161176257
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10455783	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10455784	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1084653	0.89[ASN][1000 genomes]
rs11756055	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11758404	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194271	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12206847	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12214254	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1247559	0.87[ASN][1000 genomes]
rs1247560	0.87[ASN][1000 genomes]
rs1247564	0.87[ASN][1000 genomes]
rs1247565	0.87[ASN][1000 genomes]
rs1247567	0.83[ASN][1000 genomes]
rs12526591	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1271391	0.87[ASN][1000 genomes]
rs13192114	0.81[ASN][1000 genomes]
rs13192211	0.82[ASN][1000 genomes]
rs13202192	0.83[EUR][1000 genomes]
rs13203571	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13206066	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13216458	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1344729	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1344730	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1344731	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1358755	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1367216	0.85[ASN][1000 genomes]
rs1549741	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1590185	0.84[EUR][1000 genomes]
rs1611873	0.87[ASN][1000 genomes]
rs1620969	0.87[ASN][1000 genomes]
rs1652456	0.91[JPT][hapmap]
rs1652481	0.87[ASN][1000 genomes]
rs1652498	0.87[ASN][1000 genomes]
rs1652501	0.87[ASN][1000 genomes]
rs1740445	0.87[ASN][1000 genomes]
rs1740447	0.85[ASN][1000 genomes]
rs1782627	0.87[ASN][1000 genomes]
rs1782628	0.88[ASN][1000 genomes]
rs1782629	0.87[ASN][1000 genomes]
rs1835344	0.82[EUR][1000 genomes]
rs1835345	0.81[CEU][hapmap]
rs1853022	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1965092	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991598	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991599	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2115869	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2115870	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115871	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2144727	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465835	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2465836	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs28408689	0.80[EUR][1000 genomes]
rs34797199	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757017	0.81[CHB][hapmap]
rs4440440	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4708878	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4708881	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4708882	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4708884	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4708886	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4708887	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4708888	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4708889	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4708891	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4708892	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4708893	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4709466	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709467	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709469	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709470	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66496533	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7450979	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7454268	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs783176	0.84[CHB][hapmap]
rs9355840	0.80[CEU][hapmap]
rs9456586	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9456587	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9456588	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9456589	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9456590	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9456592	0.82[EUR][1000 genomes]
rs9458025	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9458026	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9458029	0.80[EUR][1000 genomes]
rs9458030	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9458031	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9458035	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9458036	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9458039	0.84[EUR][1000 genomes]
rs9458040	0.83[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	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1019113	chr6:161127584-161197558	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3352911	chr6:161140543-161324358	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv7987	chr6:161175192-161176650	Enhancers Weak transcription Bivalent Enhancer Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9458023	LOC729603	cis	parietal	SCAN
rs9458023	SLC22A2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161169600-161181400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:161171400-161187800	Weak transcription	Pancreas	Pancrea
3	chr6:161171800-161176400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:161171800-161176400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:161175200-161178800	Weak transcription	Liver	Liver

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