Variant report

Variant	rs1942507
Chromosome Location	chr11:104554666-104554667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10502036	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10502037	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10502041	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791717	0.89[EUR][1000 genomes]
rs10791719	0.95[EUR][1000 genomes]
rs10895705	0.85[EUR][1000 genomes]
rs10895706	0.89[EUR][1000 genomes]
rs10895707	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10895708	0.92[EUR][1000 genomes]
rs10895711	0.95[EUR][1000 genomes]
rs10895712	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10895713	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10895714	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10895715	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10895719	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895721	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226426	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11226428	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11226430	0.90[EUR][1000 genomes]
rs11226431	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11226433	0.92[EUR][1000 genomes]
rs11226439	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11226441	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11226442	0.95[EUR][1000 genomes]
rs11226443	0.94[EUR][1000 genomes]
rs11226445	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11226448	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11226450	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11226452	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11226456	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11226457	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11226459	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11226460	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11226469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11226486	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1147010	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1147024	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11607612	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1200613	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1200618	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1201816	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12286808	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12361024	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12364844	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12365448	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12366152	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12418899	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12799900	0.95[EUR][1000 genomes]
rs12803385	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12803710	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1586464	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16894	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17102731	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17102776	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1893461	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1942502	0.95[EUR][1000 genomes]
rs1942520	0.95[EUR][1000 genomes]
rs1942521	0.95[EUR][1000 genomes]
rs2156127	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187131	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2187132	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2187135	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2226749	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850817	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34526738	0.92[EUR][1000 genomes]
rs34793132	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55779335	0.90[EUR][1000 genomes]
rs56384112	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59832858	0.90[EUR][1000 genomes]
rs61893183	0.95[EUR][1000 genomes]
rs61893194	0.95[EUR][1000 genomes]
rs61893228	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61893229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119997	0.95[EUR][1000 genomes]
rs722354	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7927206	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7935104	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7939905	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9666573	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9667051	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1054278	chr11:104317164-104562129	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1053886	chr11:104328822-104562129	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1037091	chr11:104330237-104559477	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv556216	chr11:104333651-104560789	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	esv3477297	chr11:104547543-104556138	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
12	esv3498988	chr11:104547556-104556135	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	inside rSNPs	n/a
13	esv3477308	chr11:104547560-104556133	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
14	esv3498989	chr11:104547560-104556133	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
15	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
16	nsv975975	chr11:104551109-104557341	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1942507	CASP1	Cis_1M	lymphoblastoid	RTeQTL
rs1942507	CASP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104550600-104555600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr11:104550600-104557800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:104551000-104555400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:104551200-104555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:104551200-104555800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:104551400-104555400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:104551600-104555600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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