Variant report

Variant	rs516536
Chromosome Location	chr11:63136501-63136502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:63136341-63136879	HepG2	liver:	n/a	chr11:63136515-63136526
2	FOXA2	chr11:63136385-63137612	HepG2	liver:	n/a	n/a
3	CEBPB	chr11:63136436-63136636	A549	lung:	n/a	chr11:63136515-63136526
4	MYBL2	chr11:63136496-63137526	HepG2	liver:	n/a	n/a
5	CEBPB	chr11:63136413-63136622	K562	blood:	n/a	chr11:63136515-63136526
6	ARID3A	chr11:63136377-63137349	HepG2	liver:	n/a	chr11:63137038-63137054
7	CEBPB	chr11:63136350-63136649	IMR90	lung:	n/a	chr11:63136515-63136526

Variant related genes	Relation type
SLC22A9	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10750998	0.95[ASN][1000 genomes]
rs10792406	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10897381	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897383	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap]
rs10897384	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap]
rs10897396	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap]
rs10897397	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs10897399	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897407	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11231397	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11231409	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231410	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231411	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231412	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11231413	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1152244	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1152245	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1152246	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11605137	0.94[ASN][1000 genomes]
rs1193718	0.80[ASN][1000 genomes]
rs1193726	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1193733	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1193786	0.88[ASN][1000 genomes]
rs1193787	0.91[ASN][1000 genomes]
rs1193891	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap]
rs1193892	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs1193904	0.80[AMR][1000 genomes]
rs1193905	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1201559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12283500	0.98[ASN][1000 genomes]
rs12293171	0.92[ASN][1000 genomes]
rs12574223	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1300798	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1404608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1525064	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1525071	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1723213	0.80[ASN][1000 genomes]
rs1723219	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1783634	0.80[ASN][1000 genomes]
rs1789334	0.80[ASN][1000 genomes]
rs1790218	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1790226	0.92[ASN][1000 genomes]
rs1944086	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317089	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2510590	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2958546	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3891629	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs3915142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3937020	0.84[EUR][1000 genomes]
rs4121881	0.99[ASN][1000 genomes]
rs4445638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs471044	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs474096	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs474191	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs474815	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs474874	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs483012	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs486460	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs488803	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494608	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4963252	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4963385	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs4963405	0.94[ASN][1000 genomes]
rs499003	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs502642	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs505653	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs510547	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511480	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs513338	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs515213	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs517655	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524724	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs526686	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs527027	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs527869	0.84[EUR][1000 genomes]
rs532085	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs534799	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs538309	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs540141	0.84[EUR][1000 genomes]
rs543429	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs548885	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs549144	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs556730	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557658	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs557879	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs558472	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs563948	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs564917	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565787	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs566456	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572017	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs575009	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs576641	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6591778	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs688999	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7126435	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap]
rs7130728	0.80[ASN][1000 genomes]
rs722508	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap]
rs7949840	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv1053585	chr11:63057767-63180308	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv555178	chr11:63078742-63197930	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs516536	DNAJC4	cis	parietal	SCAN
rs516536	SLC22A25	cis	Esophagus Mucosa	GTEx
rs516536	STX5	cis	parietal	SCAN
rs516536	SLC22A10	cis	Esophagus Muscularis	GTEx
rs516536	SDHAF2	cis	parietal	SCAN
rs516536	ACTN3	cis	cerebellum	SCAN
rs516536	CD6	cis	cerebellum	SCAN
rs516536	EFEMP2	cis	parietal	SCAN
rs516536	TSGA10IP	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63136400-63136600	Enhancers	Liver	Liver
2	chr11:63136400-63137200	Flanking Active TSS	HepG2	liver

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