Variant report

Variant	rs9458036
Chromosome Location	chr6:161213047-161213048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10455783	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10455784	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11756055	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11758404	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194271	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12214254	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1247559	0.82[ASN][1000 genomes]
rs1247560	0.82[ASN][1000 genomes]
rs1247564	0.82[ASN][1000 genomes]
rs1247565	0.82[ASN][1000 genomes]
rs1247567	0.83[ASN][1000 genomes]
rs1247572	0.92[ASN][1000 genomes]
rs12526591	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1271391	0.81[ASN][1000 genomes]
rs13192114	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13192211	0.85[ASN][1000 genomes]
rs13202192	0.94[EUR][1000 genomes]
rs13203571	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13206066	0.80[EUR][1000 genomes]
rs13216458	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1344729	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1344730	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1344731	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1358755	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549741	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590185	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1620969	0.81[ASN][1000 genomes]
rs1652456	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1652481	0.81[ASN][1000 genomes]
rs1652498	0.81[ASN][1000 genomes]
rs1652501	0.81[ASN][1000 genomes]
rs1740430	0.92[ASN][1000 genomes]
rs1740431	0.92[ASN][1000 genomes]
rs1740445	0.81[ASN][1000 genomes]
rs1740466	0.87[ASN][1000 genomes]
rs1782627	0.81[ASN][1000 genomes]
rs1782628	0.81[ASN][1000 genomes]
rs1782629	0.81[ASN][1000 genomes]
rs1835344	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1835345	0.85[CEU][hapmap]
rs1853022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1965092	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1991598	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1991599	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2115869	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2115870	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2115871	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2144727	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2465835	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2465836	0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs28408689	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34382646	0.84[ASN][1000 genomes]
rs34797199	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4440440	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4708878	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4708881	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4708882	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4708884	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4708886	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4708887	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4708888	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4708889	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4708891	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4708892	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4708893	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4709466	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4709467	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4709469	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4709470	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66496533	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7450979	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7454268	0.81[EUR][1000 genomes]
rs765351	0.81[CEU][hapmap]
rs783176	0.85[CHD][hapmap]
rs9355840	0.84[CEU][hapmap]
rs9456586	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9456587	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9456588	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456589	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456590	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9456592	0.93[EUR][1000 genomes]
rs9458023	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9458025	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9458026	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9458030	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9458031	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9458035	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9458039	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9458040	0.94[EUR][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	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	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
4	nsv830853	chr6:161180005-161376481	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv886815	chr6:161213047-161258658	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9458036	MAP3K4	cis	lymphoblastoid	seeQTL
rs9458036	LOC729603	cis	parietal	SCAN
rs9458036	SLC22A2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161211600-161213600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:161211600-161216400	Weak transcription	Esophagus	oesophagus
3	chr6:161211600-161216400	Weak transcription	Placenta	Placenta
4	chr6:161211800-161213200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:161211800-161213600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:161211800-161214800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:161212000-161213600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:161212000-161213800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:161212200-161214000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:161212200-161214200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:161212400-161214000	Enhancers	HMEC	breast
12	chr6:161212800-161213600	Enhancers	A549	lung
13	chr6:161212800-161214200	Flanking Active TSS	K562	blood
14	chr6:161212800-161215200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:161213000-161213200	Enhancers	GM12878-XiMat	blood
16	chr6:161213000-161214000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:161213000-161214200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:161213000-161214200	Enhancers	NHEK	skin

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