Variant report

Variant	rs10895707
Chromosome Location	chr11:104443208-104443209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CASP12-1	chr11:104442804-104443213	NONHSAT023935

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10502036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502037	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10502041	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10791717	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791719	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791720	0.82[EUR][1000 genomes]
rs10895705	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895706	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895708	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895711	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895712	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895713	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10895714	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895715	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10895719	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10895721	0.88[EUR][1000 genomes]
rs11226411	0.83[EUR][1000 genomes]
rs11226426	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11226428	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11226430	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11226433	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226439	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11226441	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11226442	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226443	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226445	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11226448	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11226450	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11226451	0.82[EUR][1000 genomes]
rs11226452	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11226456	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11226457	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11226459	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11226460	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11226469	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11226486	0.81[EUR][1000 genomes]
rs1147010	0.88[EUR][1000 genomes]
rs1147024	0.81[EUR][1000 genomes]
rs11601632	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11607612	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1200613	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1201816	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12286808	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12361024	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364844	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12365448	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12366152	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12418899	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12799900	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12803385	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803710	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1487689	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1586464	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17102731	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17102776	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1893461	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1942502	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1942507	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1942520	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1942521	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2156127	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2187131	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2187132	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2187135	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2226749	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850817	0.88[EUR][1000 genomes]
rs34526738	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34793132	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35510904	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55779335	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56384112	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59832858	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61893183	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61893194	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61893228	0.87[EUR][1000 genomes]
rs61893229	0.88[EUR][1000 genomes]
rs7119997	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs722354	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927206	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935104	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7939905	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9666573	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9667051	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043976	chr11:103881236-104526403	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv898352	chr11:104274535-104452042	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv898353	chr11:104274535-104497607	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv428579	chr11:104298339-104459797	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	nsv1048500	chr11:104348766-104548809	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10895707	CASP4	Cis_1M	lymphoblastoid	RTeQTL
rs10895707	CARD16	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104440400-104445200	Enhancers	Muscle Satellite Cultured Cells	--
2	chr11:104441000-104444600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:104441600-104443400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:104441600-104443400	Weak transcription	HMEC	breast
5	chr11:104441600-104443600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:104441600-104444400	Weak transcription	NHDF-Ad	bronchial
7	chr11:104441600-104444400	Weak transcription	NHEK	skin
8	chr11:104441600-104444600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:104442200-104443400	Weak transcription	HSMM	muscle
10	chr11:104442800-104444000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:104442800-104444600	Enhancers	Hela-S3	cervix
12	chr11:104443000-104443400	Enhancers	HUVEC	blood vessel
13	chr11:104443000-104444000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:104443000-104445000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links