Variant report

Variant	rs561999
Chromosome Location	chr11:104747317-104747318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10895740	0.88[EUR][1000 genomes]
rs10895742	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11226540	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11226546	0.86[JPT][hapmap]
rs11226547	0.86[JPT][hapmap]
rs11226550	0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs11605849	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12418917	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12421345	0.87[ASN][1000 genomes]
rs12422201	0.86[JPT][hapmap]
rs17103153	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2005513	0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs478650	0.81[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs491011	0.86[JPT][hapmap]
rs491945	0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs528641	0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs532705	0.86[JPT][hapmap]
rs548968	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs549691	0.86[JPT][hapmap]
rs573894	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs579156	0.83[CHB][hapmap]
rs595395	0.81[CHD][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap]
rs626771	0.86[JPT][hapmap]
rs641046	0.85[JPT][hapmap]
rs656251	0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs693312	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv826072	chr11:104662708-104768357	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832255	chr11:104674918-104846961	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	esv2757474	chr11:104719593-104798545	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2759862	chr11:104719593-104798545	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv8869	chr11:104724605-104760037	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3465886	chr11:104724810-104759731	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3465897	chr11:104724823-104759731	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3465908	chr11:104724823-104759731	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3693098	chr11:104728524-104759546	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv898355	chr11:104730322-104897843	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs561999	CASP12	cis	cerebellum	SCAN
rs561999	CASP1	Cis_1M	lymphoblastoid	RTeQTL
rs561999	PDGFD	cis	parietal	SCAN
rs561999	CASP4	Cis_1M	lymphoblastoid	RTeQTL
rs561999	CASP1///COP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104744200-104761000	Weak transcription	Aorta	Aorta
2	chr11:104745400-104749200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:104745600-104768600	Weak transcription	Left Ventricle	heart
4	chr11:104746000-104747600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:104746000-104749000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:104746200-104747600	Enhancers	Primary T cells from cord blood	blood
7	chr11:104746200-104747600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr11:104746400-104747800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr11:104746400-104748600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr11:104746400-104749200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:104746600-104747600	Enhancers	Primary B cells from cord blood	blood
12	chr11:104746600-104747600	Enhancers	Primary B cells from peripheral blood	blood
13	chr11:104746600-104749000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:104746600-104749000	Enhancers	GM12878-XiMat	blood
15	chr11:104746600-104749200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr11:104746800-104747600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:104746800-104747800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:104746800-104748400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:104747000-104747400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr11:104747000-104747800	Enhancers	Small Intestine	intestine
21	chr11:104747000-104748000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr11:104747000-104748000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr11:104747000-104748000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr11:104747000-104748000	Flanking Active TSS	Dnd41	blood
25	chr11:104747000-104748400	Enhancers	Primary hematopoietic stem cells	blood
26	chr11:104747200-104747600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr11:104747200-104747600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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