Variant report

Variant	rs6545969
Chromosome Location	chr2:62891474-62891475
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	chr2:62891427-62891648	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr2:62891350-62891849	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr2:62891470-62892163	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr2:62889516-62892400	SK-N-SH	brain:	n/a	chr2:62889587-62889601 chr2:62890249-62890258 chr2:62891356-62891370 chr2:62891753-62891767 chr2:62889967-62889976
5	TCF12	chr2:62889568-62891548	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr2:62891435-62892229	IMR90	lung:	n/a	chr2:62891752-62891765 chr2:62891752-62891763

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62883737..62887558-chr2:62889986..62892467,3	K562	blood:

Variant related genes	Relation type
ENSG00000226622	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10168771	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10172216	0.89[ASN][1000 genomes]
rs10174703	0.82[ASN][1000 genomes]
rs10177638	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10179232	0.86[ASN][1000 genomes]
rs1038572	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs10496099	0.83[EUR][1000 genomes]
rs11125941	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682530	0.93[JPT][hapmap]
rs11688816	0.93[JPT][hapmap];0.83[YRI][hapmap]
rs11893614	0.89[ASN][1000 genomes]
rs12328837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12989754	0.93[JPT][hapmap]
rs13013218	0.86[JPT][hapmap]
rs13423306	0.85[ASN][1000 genomes]
rs1386399	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1386401	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1487074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527959	0.89[ASN][1000 genomes]
rs1534418	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1534419	0.91[CEU][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1534420	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1553832	0.93[JPT][hapmap]
rs17027429	0.83[YRI][hapmap]
rs1830260	0.89[ASN][1000 genomes]
rs1843779	0.89[ASN][1000 genomes]
rs1872789	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1872790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs189671	0.93[JPT][hapmap]
rs2080227	0.83[YRI][hapmap]
rs2129509	0.89[ASN][1000 genomes]
rs2136737	0.93[JPT][hapmap]
rs2204655	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2204656	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2421713	0.88[ASN][1000 genomes]
rs2901516	0.86[ASN][1000 genomes]
rs360797	0.83[YRI][hapmap]
rs360799	0.93[JPT][hapmap];0.95[YRI][hapmap]
rs360800	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs360801	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs360804	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs360807	0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4449117	0.87[ASN][1000 genomes]
rs4461246	0.93[JPT][hapmap]
rs4479415	0.89[ASN][1000 genomes]
rs4671050	0.93[JPT][hapmap]
rs6545965	0.89[ASN][1000 genomes]
rs6545967	0.88[ASN][1000 genomes]
rs6545968	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6545971	0.93[JPT][hapmap]
rs6705835	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6706506	0.89[ASN][1000 genomes]
rs6727888	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749020	0.89[ASN][1000 genomes]
rs6752010	0.89[ASN][1000 genomes]
rs6757128	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349258	0.89[ASN][1000 genomes]
rs7421841	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7557501	0.83[YRI][hapmap]
rs7567923	0.83[YRI][hapmap]
rs7573756	0.93[JPT][hapmap];0.83[YRI][hapmap]
rs9678363	0.87[ASN][1000 genomes]
rs974344	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs974345	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545969	CCT4	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62882000-62892000	Weak transcription	Fetal Intestine Large	intestine
2	chr2:62886400-62893400	Enhancers	HMEC	breast
3	chr2:62886600-62892800	Enhancers	Osteobl	bone
4	chr2:62886600-62894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:62886600-62894200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:62886800-62892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:62887200-62894000	Enhancers	HepG2	liver
8	chr2:62887400-62894000	Enhancers	Colon Smooth Muscle	Colon
9	chr2:62887400-62899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:62887600-62892000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:62887600-62893600	Enhancers	Rectal Smooth Muscle	rectum
12	chr2:62888000-62891600	Enhancers	Fetal Kidney	kidney
13	chr2:62888000-62893800	Enhancers	Fetal Lung	lung
14	chr2:62888200-62891800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:62888600-62891800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:62888600-62892000	Weak transcription	Esophagus	oesophagus
17	chr2:62888600-62892400	Weak transcription	Pancreas	Pancrea
18	chr2:62888600-62893200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:62888600-62893200	Enhancers	NHEK	skin
20	chr2:62888800-62891800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:62888800-62892200	Enhancers	HSMM	muscle
22	chr2:62889200-62891800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:62889200-62892200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:62889200-62892400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:62889400-62891600	Enhancers	Brain Hippocampus Middle	brain
26	chr2:62889400-62892200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:62889400-62892200	Enhancers	HSMMtube	muscle
28	chr2:62889400-62893000	Enhancers	Adipose Nuclei	Adipose
29	chr2:62889600-62892200	Enhancers	Fetal Brain Male	brain
30	chr2:62889600-62892400	Enhancers	A549	lung
31	chr2:62889600-62894000	Enhancers	Fetal Stomach	stomach
32	chr2:62889800-62891800	Weak transcription	Lung	lung
33	chr2:62889800-62892200	Enhancers	NH-A	brain
34	chr2:62890000-62892200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:62890000-62892200	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:62890000-62892600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:62890000-62893000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:62890000-62893400	Enhancers	Liver	Liver
39	chr2:62890000-62899000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:62890000-62899800	Weak transcription	Right Atrium	heart
41	chr2:62890400-62899000	Weak transcription	Ovary	ovary
42	chr2:62890600-62893200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:62890800-62891800	Enhancers	Fetal Heart	heart
44	chr2:62890800-62892200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:62890800-62892400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:62890800-62893200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr2:62890800-62893200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:62891000-62891600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:62891000-62891600	Flanking Active TSS	NHDF-Ad	bronchial
50	chr2:62891000-62892000	Weak transcription	Brain Inferior Temporal Lobe	brain

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