Variant report

Variant	rs920573
Chromosome Location	chr11:59924959-59924960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs107903	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10897009	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897011	0.82[EUR][1000 genomes]
rs11230147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11230153	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11230155	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11230160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11230161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11230180	0.82[EUR][1000 genomes]
rs1125357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151104	1.00[CHB][hapmap]
rs11600716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605427	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12226022	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs1286169	1.00[CHB][hapmap]
rs1303615	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs1303621	0.85[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs1441586	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs17528859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17529983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17602572	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs1786137	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1813217	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1820430	0.82[EUR][1000 genomes]
rs1834549	0.82[EUR][1000 genomes]
rs1834550	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1834551	0.82[EUR][1000 genomes]
rs1834557	0.81[EUR][1000 genomes]
rs2070970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2081545	0.82[EUR][1000 genomes]
rs2165525	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278867	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs2583471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2583476	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2847655	1.00[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2847663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2847664	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2847666	1.00[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2847667	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2847668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2855017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs474951	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs476722	0.85[CEU][hapmap]
rs483629	0.87[EUR][1000 genomes]
rs487997	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4939311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4939312	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4939314	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501697	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs502419	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs502581	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs504272	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs510518	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs512495	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs514266	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs516478	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs521952	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs525794	0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs528823	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs534273	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs539360	1.00[CHB][hapmap]
rs540170	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs555635	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs556917	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs55847558	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs558678	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs558788	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs56189574	0.86[ASN][1000 genomes]
rs56201148	0.82[EUR][1000 genomes]
rs563803	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs564912	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs569046	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs574695	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs574704	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs574798	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs579721	1.00[CHB][hapmap]
rs580817	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs581133	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs583296	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs595481	0.84[CEU][hapmap]
rs602396	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs606588	0.87[CEU][hapmap]
rs617916	0.84[CEU][hapmap]
rs61901691	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs652354	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs684961	0.85[CEU][hapmap]
rs688030	0.88[CEU][hapmap]
rs7124974	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72918674	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7926344	0.80[EUR][1000 genomes]
rs7926354	0.80[EUR][1000 genomes]
rs7926729	0.80[EUR][1000 genomes]
rs7926954	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7933202	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7935829	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs7946992	0.84[EUR][1000 genomes]
rs983392	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv33843	chr11:59908131-59945334	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs920573	SCGB2A2	cis	cerebellum	SCAN
rs920573	POLR2G	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59924000-59926400	Weak transcription	HUVEC	blood vessel
2	chr11:59924000-59930800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:59924000-59932800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:59924800-59929800	Strong transcription	Monocytes-CD14+_RO01746	blood

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