Variant report

Variant	rs4752801
Chromosome Location	chr11:47907641-47907642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10838747	0.89[CEU][hapmap]
rs10838748	0.89[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs10838757	0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap]
rs11039416	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11039426	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11039433	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11605774	0.82[AMR][1000 genomes]
rs12361256	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12364432	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12418852	0.89[CEU][hapmap];0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12785833	0.82[AMR][1000 genomes]
rs12798109	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17788930	0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs2290850	0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs34128973	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34614231	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35985502	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752797	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752873	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7105282	0.89[CEU][hapmap];0.84[CHB][hapmap]
rs7927771	0.89[CEU][hapmap]
rs7947730	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs9909	0.89[CEU][hapmap];0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4752801	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs4752801	MTCH2	cis	cerebellum	SCAN
rs4752801	SLC35C1	cis	parietal	SCAN
rs4752801	C1QTNF4	cis	lymphoblastoid	seeQTL
rs4752801	C1QTNF4	cis	Muscle Skeletal	GTEx
rs4752801	Hs.6637	cis	multi-tissue	Pritchard
rs4752801	C1QTNF4	cis	multi-tissue	Pritchard
rs4752801	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs4752801	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4752801	FNBP4	cis	lesional skin	skin_eQTL
rs4752801		cis	Lymphoblastoid	GTEx
rs4752801	ACP2	cis	lymphoblastoid	seeQTL
rs4752801	MADD	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47903200-47913400	Weak transcription	Hela-S3	cervix
2	chr11:47905400-47908600	Enhancers	Placenta	Placenta
3	chr11:47905400-47912400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr11:47906000-47910400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr11:47906000-47912200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:47906000-47912400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr11:47906200-47908200	Enhancers	Fetal Thymus	thymus
8	chr11:47906200-47908800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr11:47906200-47911800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:47906200-47912000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr11:47906200-47912200	Enhancers	Primary T cells from cord blood	blood
12	chr11:47906400-47908200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:47906600-47908000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr11:47906800-47908400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr11:47907000-47907800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:47907000-47907800	Enhancers	Fetal Intestine Large	intestine
17	chr11:47907000-47907800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr11:47907000-47907800	Enhancers	Thymus	Thymus
19	chr11:47907000-47907800	Enhancers	NHDF-Ad	bronchial
20	chr11:47907000-47907800	Enhancers	NHLF	lung
21	chr11:47907000-47908000	Enhancers	Primary B cells from peripheral blood	blood
22	chr11:47907000-47908000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:47907000-47908000	Enhancers	Adipose Nuclei	Adipose
24	chr11:47907000-47908000	Enhancers	Fetal Stomach	stomach
25	chr11:47907000-47908000	Enhancers	HepG2	liver
26	chr11:47907000-47908000	Enhancers	HSMMtube	muscle
27	chr11:47907000-47908200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:47907000-47908200	Enhancers	Fetal Intestine Small	intestine
29	chr11:47907200-47907800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:47907200-47907800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:47907200-47907800	Enhancers	Dnd41	blood
32	chr11:47907200-47908000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr11:47907400-47907800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:47907400-47907800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:47907400-47907800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr11:47907400-47907800	Flanking Active TSS	A549	lung
37	chr11:47907400-47907800	Flanking Active TSS	HUVEC	blood vessel
38	chr11:47907400-47907800	Enhancers	NH-A	brain
39	chr11:47907400-47907800	Flanking Active TSS	Osteobl	bone
40	chr11:47907400-47908000	Enhancers	Primary B cells from cord blood	blood
41	chr11:47907400-47908000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr11:47907600-47907800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:47907600-47907800	Enhancers	HSMM	muscle
44	chr11:47907600-47908000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:47907600-47911200	Weak transcription	Primary hematopoietic stem cells	blood

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