Variant report

Variant	rs4752839
Chromosome Location	chr11:47495202-47495203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47495027-47495336	K562	blood:	n/a	n/a
2	POLR2A	chr11:47495136-47495290	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47492716..47498082-chr11:47498479..47503693,7	MCF-7	breast:

Variant related genes	Relation type
CELF1	TF binding region
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1044269	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1051006	0.81[CEU][hapmap]
rs10742805	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs10742806	0.89[JPT][hapmap]
rs10742816	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs10769253	0.81[CEU][hapmap]
rs10769255	0.91[CEU][hapmap]
rs10838689	0.81[CEU][hapmap]
rs11039278	0.82[AMR][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11820650	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11821273	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11821860	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11821917	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11822402	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11823490	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11824864	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11824971	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11824990	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11828339	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12419342	0.89[JPT][hapmap]
rs1474056	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs17198158	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17790804	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2138767	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs2242511	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2290148	0.81[CEU][hapmap]
rs3729802	0.85[CEU][hapmap]
rs3740684	0.84[GIH][hapmap];0.84[JPT][hapmap]
rs3781628	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3824867	0.81[GIH][hapmap];0.89[JPT][hapmap]
rs3847503	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147730	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs4237544	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs4282946	0.88[JPT][hapmap]
rs4384349	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752783	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs4752786	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs4752829	0.82[JPT][hapmap]
rs4752837	0.89[JPT][hapmap]
rs4752842	0.82[MEX][hapmap]
rs4752843	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752977	0.81[CEU][hapmap]
rs4752983	0.81[CEU][hapmap]
rs4752992	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59631865	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60882887	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60929305	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61000762	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7105122	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs7105907	0.89[JPT][hapmap]
rs7111873	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs7126210	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs753812	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs753992	0.81[CEU][hapmap]
rs7931089	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7948705	0.89[JPT][hapmap]
rs9666924	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[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	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4752839	ATG13	cis	parietal	SCAN
rs4752839	LOC441601	cis	cerebellum	SCAN
rs4752839	SLC35C1	cis	cerebellum	SCAN
rs4752839	TTC17	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47480000-47510000	Strong transcription	Thymus	Thymus
2	chr11:47480600-47508400	Strong transcription	Fetal Intestine Small	intestine
3	chr11:47480800-47511000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:47480800-47511400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:47481000-47498400	Strong transcription	NHEK	skin
6	chr11:47483400-47508800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:47483600-47511400	Strong transcription	Dnd41	blood
8	chr11:47484800-47504800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:47484800-47510600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:47484800-47511000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:47485200-47511400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:47485400-47504800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:47485400-47511400	Strong transcription	Primary B cells from cord blood	blood
14	chr11:47485600-47498800	Strong transcription	K562	blood
15	chr11:47485600-47511000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:47485800-47518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:47486000-47510000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:47486200-47511200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr11:47486200-47511200	Strong transcription	Primary T cells from cord blood	blood
20	chr11:47486400-47510200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:47486800-47496800	Strong transcription	HMEC	breast
22	chr11:47487800-47507400	Strong transcription	Fetal Intestine Large	intestine
23	chr11:47488200-47510800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:47488200-47511200	Strong transcription	GM12878-XiMat	blood
25	chr11:47488400-47509000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:47488400-47509800	Strong transcription	Placenta	Placenta
27	chr11:47488800-47510800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr11:47489000-47501000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:47489200-47500800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:47489200-47508400	Strong transcription	Fetal Stomach	stomach
31	chr11:47489200-47508800	Strong transcription	Spleen	Spleen
32	chr11:47489200-47510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:47489200-47522800	Strong transcription	Fetal Thymus	thymus
34	chr11:47489400-47495600	Strong transcription	NHLF	lung
35	chr11:47489400-47498600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:47489400-47510800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:47489600-47498800	Strong transcription	HSMM	muscle
38	chr11:47489800-47499600	Strong transcription	Fetal Kidney	kidney
39	chr11:47489800-47509200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr11:47489800-47510000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:47489800-47510600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr11:47490000-47495400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:47490000-47499800	Strong transcription	Fetal Muscle Leg	muscle
44	chr11:47490000-47509000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr11:47490000-47510600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:47490000-47511000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr11:47490200-47496600	Strong transcription	NHDF-Ad	bronchial
48	chr11:47490600-47496600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:47490600-47500600	Strong transcription	Pancreas	Pancrea
50	chr11:47490600-47508800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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