Variant report

Variant	rs11699391
Chromosome Location	chr20:16579956-16579957
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16577829..16580516-chr20:16584380..16586339,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10485558	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11697576	0.95[EUR][1000 genomes]
rs11698735	0.95[EUR][1000 genomes]
rs17675229	0.86[EUR][1000 genomes]
rs17675340	0.86[EUR][1000 genomes]
rs17681859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17744425	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17744455	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6034525	0.86[EUR][1000 genomes]
rs6034526	0.86[EUR][1000 genomes]
rs6044099	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6044101	0.86[EUR][1000 genomes]
rs6044105	0.86[EUR][1000 genomes]
rs6044108	0.86[EUR][1000 genomes]
rs6044167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs6044172	0.95[EUR][1000 genomes]
rs6111185	0.86[EUR][1000 genomes]
rs62196283	0.86[EUR][1000 genomes]
rs62196284	0.86[EUR][1000 genomes]
rs62196285	0.82[EUR][1000 genomes]
rs62196286	0.86[EUR][1000 genomes]
rs62196289	0.86[EUR][1000 genomes]
rs62196304	0.86[EUR][1000 genomes]
rs62196305	0.86[EUR][1000 genomes]
rs62196307	0.86[EUR][1000 genomes]
rs62196308	0.86[EUR][1000 genomes]
rs62196310	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517032	chr20:16560990-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	nsv585650	chr20:16561203-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv1057674	chr20:16564642-16593209	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv2760669	chr20:16564654-16587606	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv1061216	chr20:16564668-16586544	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv1060264	chr20:16565162-16586544	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv3454156	chr20:16566305-16586918	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	esv3454158	chr20:16566325-16586923	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	esv3454157	chr20:16566369-16586867	Bivalent Enhancer Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	esv3454159	chr20:16566398-16586879	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	esv3454160	chr20:16566441-16586777	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv16895	chr20:16566460-16586787	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv3693287	chr20:16567202-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
14	nsv438309	chr20:16567202-16585314	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	nsv458936	chr20:16567202-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv458937	chr20:16567202-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
17	nsv458938	chr20:16567202-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv585651	chr20:16567202-16585314	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv817887	chr20:16567202-16585314	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
20	esv2421920	chr20:16567202-16586634	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
21	nsv470542	chr20:16567202-16588308	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
22	nsv442482	chr20:16568058-16586634	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
23	nsv1057376	chr20:16568062-16586067	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
24	nsv1059010	chr20:16568062-16586544	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
25	nsv1055217	chr20:16568062-16596470	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
26	nsv458939	chr20:16568129-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
27	nsv458941	chr20:16568129-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
28	nsv585652	chr20:16568129-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
29	nsv458942	chr20:16568129-16589003	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
30	nsv585653	chr20:16568129-16589003	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
31	nsv585654	chr20:16568537-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
32	nsv514935	chr20:16571383-16586590	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
33	nsv1060877	chr20:16575001-16586544	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
34	nsv1061807	chr20:16575463-16586544	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
35	nsv1064197	chr20:16575463-16587230	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
36	nsv1062741	chr20:16575531-16586544	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11699391	IL9	trans	lymphoblastoid	seeQTL
rs11699391	ALDH1A3	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16578800-16580600	Weak transcription	Fetal Brain Male	brain

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