Variant report

Variant	rs11687292
Chromosome Location	chr2:231099204-231099205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11679983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11695193	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17263269	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329429	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329583	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56063375	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56334214	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11687292	ECEL1	cis	cerebellum	SCAN
rs11687292	USP40	cis	cerebellum	SCAN
rs11687292	IL10RB	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231091000-231102600	Weak transcription	Small Intestine	intestine
3	chr2:231092600-231118400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:231093200-231113000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:231096000-231101600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:231096000-231102600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:231096200-231101600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:231096400-231100200	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr2:231097200-231099600	Weak transcription	NH-A	brain
10	chr2:231097600-231101200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:231098000-231108200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:231098200-231100200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:231098400-231100200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr2:231098600-231099600	Flanking Active TSS	GM12878-XiMat	blood
15	chr2:231098600-231100400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:231098600-231107400	Strong transcription	Primary B cells from cord blood	blood
17	chr2:231098800-231099800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:231098800-231100000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:231098800-231100200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:231099000-231099800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:231099000-231099800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:231099200-231099600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:231099200-231101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:231099200-231109000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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