Variant report

Variant	rs11520906
Chromosome Location	chr7:145935428-145935429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10230226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10237336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10256834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10263587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10265805	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10268545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10277217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10428910	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10500163	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11974152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11978140	0.97[ASN][1000 genomes]
rs11980028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12333427	0.85[JPT][hapmap]
rs12703770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12703779	0.93[ASN][1000 genomes]
rs12703780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12703781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12703784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12703785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12703786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12703788	0.97[ASN][1000 genomes]
rs12703790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12703791	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13221011	0.97[ASN][1000 genomes]
rs13223353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13223500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13223589	0.93[ASN][1000 genomes]
rs13224076	0.97[ASN][1000 genomes]
rs13224126	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs13224183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13224771	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13238577	0.97[ASN][1000 genomes]
rs13239694	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13241192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13242084	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242684	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13245661	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405115	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1464959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1464960	0.97[ASN][1000 genomes]
rs1464961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1526079	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17169989	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17169990	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17402725	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17577839	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1917936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2014200	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2030836	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2080179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2080180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2098288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2140950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2430324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2430328	0.90[ASN][1000 genomes]
rs2462829	0.82[ASN][1000 genomes]
rs2462830	0.97[ASN][1000 genomes]
rs2539738	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2539739	0.97[ASN][1000 genomes]
rs2539740	0.97[ASN][1000 genomes]
rs2539744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2539745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2539746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2539747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2693306	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs2693307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28600774	0.97[ASN][1000 genomes]
rs34053851	0.80[ASN][1000 genomes]
rs34276665	1.00[ASN][1000 genomes]
rs34332205	1.00[ASN][1000 genomes]
rs35018596	1.00[ASN][1000 genomes]
rs35273012	1.00[ASN][1000 genomes]
rs35491208	1.00[ASN][1000 genomes]
rs36018030	1.00[ASN][1000 genomes]
rs4327781	0.97[ASN][1000 genomes]
rs4345482	0.97[ASN][1000 genomes]
rs4445148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4445149	0.97[ASN][1000 genomes]
rs6464733	0.97[ASN][1000 genomes]
rs6464734	0.90[ASN][1000 genomes]
rs6464737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6464738	0.97[ASN][1000 genomes]
rs6464739	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs67518892	0.80[ASN][1000 genomes]
rs67548137	1.00[ASN][1000 genomes]
rs68099112	1.00[ASN][1000 genomes]
rs6946245	0.97[ASN][1000 genomes]
rs6947847	0.85[ASN][1000 genomes]
rs6959235	0.97[ASN][1000 genomes]
rs6960368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6960388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6960982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6966811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73160680	0.80[ASN][1000 genomes]
rs7777761	0.97[ASN][1000 genomes]
rs7779760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7780228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7785592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7785673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7786007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7787269	0.97[ASN][1000 genomes]
rs7788768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7789370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7793060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7794609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7794731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7795024	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7795190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7795488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7798919	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7811486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7811558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802530	0.97[ASN][1000 genomes]
rs802532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802534	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802535	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs802546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802547	0.88[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs802548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs802550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs802552	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs802556	0.92[CEU][hapmap]
rs802557	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs802577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs802580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs802581	0.93[ASN][1000 genomes]
rs810596	0.97[ASN][1000 genomes]
rs940932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs940933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs949953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs955107	0.97[ASN][1000 genomes]
rs955108	0.97[ASN][1000 genomes]
rs959411	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	nsv889386	chr7:145845418-145935428	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1030541	chr7:145883107-146022564	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv889387	chr7:145903862-146239545	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv5992	chr7:145922744-145967420	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv608928	chr7:145928429-145952946	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv533345	chr7:145934546-146134958	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv933622	chr7:145935381-145995971	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11520906	EPHA1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:145912600-145945200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:145918800-145942600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:145922800-145943600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:145931800-145935600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:145931800-145936600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:145931800-145937200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:145931800-145937400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:145932000-145936800	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr7:145932000-145937200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr7:145932000-145937200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:145932400-145936400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:145932800-145935800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:145935000-145936600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:145935200-145936000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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