Variant report

Variant	rs4753852
Chromosome Location	chr11:108766706-108766707
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10466523	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10502106	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10749926	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10749927	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs10749928	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[EUR][1000 genomes]
rs10749929	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs10789676	0.85[EUR][1000 genomes]
rs10789677	0.84[EUR][1000 genomes]
rs10789678	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10789680	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10789681	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs10789682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs10789683	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs10789685	0.91[EUR][1000 genomes]
rs10789688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10789691	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10789693	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10789694	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10789696	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10890879	0.85[EUR][1000 genomes]
rs10890883	0.85[EUR][1000 genomes]
rs10890888	0.85[EUR][1000 genomes]
rs10890889	0.88[EUR][1000 genomes]
rs10890893	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs10890894	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs10890895	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890897	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890898	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890901	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890902	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890903	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890908	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10890909	0.81[ASN][1000 genomes]
rs11212771	1.00[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs11212774	0.86[EUR][1000 genomes]
rs11212797	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11212802	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11212811	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11212816	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11212825	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11530525	0.85[EUR][1000 genomes]
rs12420572	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1824664	0.85[EUR][1000 genomes]
rs1824665	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1863366	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2169562	0.81[EUR][1000 genomes]
rs2357224	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3781864	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs3781866	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs3781867	0.84[EUR][1000 genomes]
rs3902843	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4027488	0.86[EUR][1000 genomes]
rs4237580	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4497371	1.00[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4753849	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4754354	0.86[EUR][1000 genomes]
rs4754357	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4754358	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4754359	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754366	0.91[ASN][1000 genomes]
rs61912810	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103086	0.86[EUR][1000 genomes]
rs7116062	0.85[EUR][1000 genomes]
rs7940595	0.85[EUR][1000 genomes]
rs890237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv898386	chr11:108409442-108831875	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv898389	chr11:108724639-108891986	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv2761707	chr11:108763836-108772204	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4753852	ZC3H12C	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108726200-108768400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr11:108728400-108810600	Weak transcription	Left Ventricle	heart
3	chr11:108757800-108766800	Weak transcription	Stomach Mucosa	stomach
4	chr11:108758400-108766800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:108760800-108767800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:108761800-108767000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:108762000-108767800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:108763000-108797600	Weak transcription	Fetal Muscle Leg	muscle
9	chr11:108764800-108767600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr11:108764800-108768000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr11:108764800-108768200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr11:108765000-108768000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr11:108765000-108768400	Enhancers	Hela-S3	cervix
14	chr11:108765600-108768600	Weak transcription	K562	blood
15	chr11:108765800-108768000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:108765800-108768800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:108766000-108766800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr11:108766000-108766800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr11:108766000-108767000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr11:108766000-108768200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:108766000-108768400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:108766200-108767000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:108766200-108767000	Active TSS	A549	lung
24	chr11:108766200-108767400	Flanking Active TSS	HUVEC	blood vessel
25	chr11:108766200-108768800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr11:108766400-108766800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr11:108766400-108767000	Active TSS	Monocytes-CD14+_RO01746	blood
28	chr11:108766400-108767200	Flanking Active TSS	Osteobl	bone
29	chr11:108766400-108767400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr11:108766400-108767400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr11:108766400-108768000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:108766400-108768000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:108766400-108768200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:108766400-108768400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:108766600-108766800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr11:108766600-108766800	Enhancers	NHEK	skin
37	chr11:108766600-108767000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:108766600-108767000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:108766600-108767000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr11:108766600-108767000	Active TSS	Adipose Nuclei	Adipose
41	chr11:108766600-108767000	Enhancers	HSMMtube	muscle
42	chr11:108766600-108767200	Enhancers	Primary B cells from cord blood	blood
43	chr11:108766600-108767200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:108766600-108767200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:108766600-108767200	Flanking Active TSS	HMEC	breast
46	chr11:108766600-108767400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:108766600-108767400	ZNF genes & repeats	GM12878-XiMat	blood
48	chr11:108766600-108767400	Enhancers	NHDF-Ad	bronchial
49	chr11:108766600-108767600	Enhancers	HSMM	muscle
50	chr11:108766600-108767600	Flanking Active TSS	NH-A	brain

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