Variant report

Variant	rs1201816
Chromosome Location	chr11:104578143-104578144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10502036	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10502037	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10502041	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10791717	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791719	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10895705	0.85[EUR][1000 genomes]
rs10895706	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10895707	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10895708	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10895711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10895712	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10895713	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10895714	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10895715	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10895719	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10895721	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11226426	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226428	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226430	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226431	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226433	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11226439	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226441	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226442	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226443	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226445	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11226448	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11226450	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11226452	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11226456	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11226457	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11226459	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11226460	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11226469	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226486	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1147010	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147024	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607612	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1200613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200618	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12286808	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12361024	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12364844	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12365448	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12366152	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12418899	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12799900	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12803385	0.88[EUR][1000 genomes]
rs12803710	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1586464	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16894	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17102731	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17102776	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893461	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1942502	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1942507	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1942520	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1942521	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2156127	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187131	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2187132	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2187135	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2226749	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850817	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34526738	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34793132	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55779335	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56384112	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59832858	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61893183	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61893194	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61893228	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61893229	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7119997	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs722354	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7927206	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7935104	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7939905	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9666573	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9667051	0.95[EUR][1000 genomes];0.91[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	nsv1044271	chr11:104136156-104666252	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1054456	chr11:104358924-104805251	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv832254	chr11:104412769-104607277	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2761706	chr11:104523335-104634024	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1050346	chr11:104548749-104664665	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1201816	CASP1	Cis_1M	lymphoblastoid	RTeQTL
rs1201816	CASP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104576400-104578800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:104576600-104580400	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr11:104576600-104580600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:104576800-104579000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:104576800-104579000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:104577000-104579000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr11:104577000-104579000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr11:104577000-104580400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr11:104577000-104580400	Weak transcription	NHLF	lung
10	chr11:104577200-104578200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr11:104577200-104578600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:104577200-104578600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:104577200-104578800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:104577200-104580600	Enhancers	Primary T cells from cord blood	blood
15	chr11:104577200-104580600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:104577400-104580600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr11:104577600-104578200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:104577600-104578600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:104577600-104580600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:104577800-104580800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr11:104578000-104578200	Enhancers	Dnd41	blood
22	chr11:104578000-104581000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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