Variant report

Variant	rs959411
Chromosome Location	chr7:145845418-145845419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10230226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10237336	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10248963	0.82[CHD][hapmap]
rs10256834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10263587	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10265805	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10268545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10277217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10428910	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10500163	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11520906	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11974152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11980028	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12333427	0.85[JPT][hapmap]
rs12703770	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12703780	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12703781	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12703784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12703785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12703786	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12703790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12703791	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13223353	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs13223500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13224126	0.83[CEU][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs13224183	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs13224771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13239694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13241192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13242084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13242684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13245661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs1405115	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1464959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1464961	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1526072	0.97[ASN][1000 genomes]
rs1526079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs17169989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17169990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17402725	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17577839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1917936	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2014200	1.00[JPT][hapmap]
rs2030836	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2080179	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2080180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2098288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2140950	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2430324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2539738	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2539744	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2539745	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2539746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2539747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2693306	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2693307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28564084	0.97[ASN][1000 genomes]
rs34038575	0.97[ASN][1000 genomes]
rs34053851	1.00[ASN][1000 genomes]
rs34276665	0.80[ASN][1000 genomes]
rs34280066	0.93[ASN][1000 genomes]
rs34332205	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35018596	0.80[ASN][1000 genomes]
rs35273012	0.80[ASN][1000 genomes]
rs35491208	0.80[ASN][1000 genomes]
rs36018030	0.80[ASN][1000 genomes]
rs4445148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6464737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6464739	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs67518892	1.00[ASN][1000 genomes]
rs67548137	0.80[ASN][1000 genomes]
rs68099112	0.80[ASN][1000 genomes]
rs6960368	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6960388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6960982	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6966811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73160680	1.00[ASN][1000 genomes]
rs7779760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7780228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7785592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7785673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7786007	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7788768	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7789370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7793060	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7794609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7794731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7794944	0.82[CHD][hapmap]
rs7795024	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7795190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7795488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7797553	0.82[CHD][hapmap]
rs7798919	1.00[JPT][hapmap]
rs7805261	0.97[ASN][1000 genomes]
rs7811486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7811558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802532	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802534	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs802535	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs802538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802539	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802543	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802546	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802547	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs802548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802556	0.85[CEU][hapmap]
rs802557	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs802577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs940932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs940933	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs949953	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889384	chr7:145541783-146239545	Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1023861	chr7:145606069-145910049	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv539170	chr7:145606069-145910049	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1020950	chr7:145683419-146264304	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv981604	chr7:145773003-145935052	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv608927	chr7:145803095-145882001	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv933697	chr7:145844438-145864611	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv889386	chr7:145845418-145935428	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs959411	ZNF467	cis	parietal	SCAN
rs959411	KRBA1	cis	parietal	SCAN
rs959411	MGAM	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:145843600-145846800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr7:145843600-145846800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr7:145843800-145847200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:145844000-145845800	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr7:145844600-145846600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:145844800-145845800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:145844800-145845800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:145845400-145845600	Enhancers	H1 Cell Line	embryonic stem cell

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