Variant report

Variant	rs11052877
Chromosome Location	chr12:9905690-9905691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9903679..9905880-chr12:10079207..10081404,2	K562	blood:
2	chr12:9902845..9905965-chr18:46122603..46125602,4	K562	blood:
3	chr12:9903687..9905772-chr12:9958368..9961230,2	K562	blood:
4	chr12:9904754..9907523-chr12:9964008..9966438,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1008610	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1044771	0.85[JPT][hapmap]
rs10466829	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10492165	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10492166	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10743823	0.86[JPT][hapmap]
rs10772085	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10772087	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10772091	0.80[ASN][1000 genomes]
rs10772092	0.80[ASN][1000 genomes]
rs10772094	0.80[ASN][1000 genomes]
rs10772102	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10772108	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10844456	0.90[JPT][hapmap]
rs10844503	0.90[JPT][hapmap]
rs10844537	0.90[JPT][hapmap]
rs10844615	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10844617	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10844620	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10844626	0.80[ASN][1000 genomes]
rs10844627	0.80[ASN][1000 genomes]
rs10844630	0.80[ASN][1000 genomes]
rs10844632	0.80[ASN][1000 genomes]
rs10844633	0.80[ASN][1000 genomes]
rs10844635	0.80[ASN][1000 genomes]
rs10844636	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10844638	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10844657	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10844682	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10844706	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11052372	0.85[JPT][hapmap]
rs11052423	0.85[JPT][hapmap]
rs11052426	0.90[JPT][hapmap]
rs11052552	0.90[JPT][hapmap]
rs11052710	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11052750	0.80[ASN][1000 genomes]
rs11052751	0.80[ASN][1000 genomes]
rs11052752	0.80[ASN][1000 genomes]
rs12227655	0.95[JPT][hapmap]
rs17806710	0.90[JPT][hapmap]
rs2080211	0.84[JPT][hapmap]
rs2098298	0.94[JPT][hapmap]
rs2114870	0.81[JPT][hapmap]
rs2268146	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2401391	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2401393	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3764021	0.85[JPT][hapmap]
rs3764022	0.85[JPT][hapmap]
rs4763840	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4763879	0.82[JPT][hapmap]
rs7296241	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7306304	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7306557	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7310460	0.85[JPT][hapmap]
rs7970116	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7973638	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7974396	0.89[JPT][hapmap]
rs917911	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv976572	chr12:9896625-9906830	Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11052877	CLEC2A	cis	parietal	SCAN
rs11052877	C12orf53	cis	parietal	SCAN
rs11052877	AICDA	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9893400-9910800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:9895600-9906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:9896400-9911000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:9903200-9905800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:9903400-9907600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:9903400-9917600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:9903600-9911000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:9903800-9911200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:9904000-9905800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:9904000-9910200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:9904200-9910800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:9904200-9911200	Weak transcription	Small Intestine	intestine
13	chr12:9904400-9913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:9904600-9905800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:9904600-9905800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:9904600-9913400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr12:9904800-9907000	Weak transcription	Thymus	Thymus
18	chr12:9904800-9908800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:9904800-9908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:9905000-9908600	Strong transcription	Primary B cells from cord blood	blood
21	chr12:9905200-9906000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:9905200-9907800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:9905200-9908600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr12:9905200-9908800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:9905200-9908800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:9905200-9908800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:9905200-9908800	Strong transcription	K562	blood
28	chr12:9905200-9909400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:9905400-9907600	Strong transcription	Dnd41	blood
30	chr12:9905400-9908800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:9905400-9908800	Strong transcription	Fetal Thymus	thymus
32	chr12:9905400-9909200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:9905600-9905800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:9905600-9906000	Enhancers	HUVEC	blood vessel
35	chr12:9905600-9907200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:9905600-9908800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr12:9905600-9908800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr12:9905600-9908800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:9905600-9908800	Strong transcription	GM12878-XiMat	blood
40	chr12:9905600-9909000	Genic enhancers	Primary T cells from cord blood	blood
41	chr12:9905600-9913400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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