Variant report

Variant	rs2513726
Chromosome Location	chr11:57798942-57798943
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	POLR2A	chr11:57798881-57799114	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
RNU6-899P	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1013447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10750876	0.89[GIH][hapmap]
rs10750877	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10750878	1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs10750882	0.89[GIH][hapmap]
rs10792126	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10792127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792128	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10792129	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10792130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896689	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896690	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10896692	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10896696	0.91[JPT][hapmap]
rs11229194	0.85[ASN][1000 genomes]
rs11229195	0.85[ASN][1000 genomes]
rs11229221	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11229236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11229237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1123196	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1123306	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1123307	0.90[JPT][hapmap]
rs12363350	0.89[GIH][hapmap]
rs1374570	0.82[JPT][hapmap]
rs1447169	0.89[GIH][hapmap]
rs1545459	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1562863	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1868043	1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2003375	0.91[JPT][hapmap]
rs2100110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2167357	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2167358	0.90[JPT][hapmap]
rs2218598	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2441950	0.91[JPT][hapmap]
rs2441958	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2441960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441972	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2441977	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2441979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2443445	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2443449	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2443450	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2513705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2513727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513728	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2513729	0.93[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2513730	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2514181	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2514186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2514187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2514191	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2514199	0.83[AFR][1000 genomes]
rs2514202	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2866830	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851119	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3974323	0.89[GIH][hapmap]
rs4938883	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4939174	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4939176	1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs4939182	0.89[GIH][hapmap]
rs6591455	0.89[GIH][hapmap]
rs7111942	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7117711	0.89[GIH][hapmap]
rs7118536	1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs7119421	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7125209	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs896300	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs921132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921133	0.84[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs921134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971066	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs976429	0.91[JPT][hapmap]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv2761678	chr11:57768288-57810886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2513726	OR8J3	cis	cerebellum	SCAN
rs2513726	MS4A6A	cis	parietal	SCAN
rs2513726	OR4C6	cis	parietal	SCAN
rs2513726	MS4A8B	cis	cerebellum	SCAN
rs2513726	YPEL4	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57792000-57811400	Weak transcription	Right Atrium	heart
2	chr11:57796400-57799200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:57797600-57799000	Weak transcription	Pancreas	Pancrea
4	chr11:57798400-57799400	ZNF genes & repeats	Lung	lung

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