Variant report

Variant	rs6539264
Chromosome Location	chr12:106691577-106691578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:106691508-106691645	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr12:106691527-106691802	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106681884..106684629-chr12:106690142..106692721,2	MCF-7	breast:
2	chr12:106637683..106639757-chr12:106691523..106693781,3	MCF-7	breast:
3	chr12:106691206..106693706-chr12:106694212..106695819,2	K562	blood:
4	chr12:106639341..106642339-chr12:106691161..106693366,2	MCF-7	breast:
5	chr12:106688729..106691851-chr12:106693637..106696966,3	MCF-7	breast:

No data

Variant related genes	Relation type
TCP11L2	TF binding region
ENSG00000166046	Chromatin interaction
ENSG00000258355	Chromatin interaction
ENSG00000136026	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10778462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10778463	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10861573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831752	0.97[ASN][1000 genomes]
rs12313045	1.00[YRI][hapmap]
rs1392176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1532586	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs2243506	0.81[GIH][hapmap]
rs2252685	0.81[GIH][hapmap]
rs2253838	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs4964460	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6539261	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6539262	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs6539263	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7296927	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297359	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298576	0.91[ASN][1000 genomes]
rs7957421	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7965616	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794382	chr12:106679812-106699151	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539264	EID3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106680000-106695200	Weak transcription	Right Atrium	heart
2	chr12:106683200-106693000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:106685800-106692800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:106685800-106695200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:106685800-106695200	Weak transcription	Fetal Lung	lung
6	chr12:106688400-106693000	Weak transcription	K562	blood
7	chr12:106689000-106695800	Weak transcription	Lung	lung
8	chr12:106689600-106691800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:106689800-106691800	Enhancers	Fetal Heart	heart
10	chr12:106689800-106691800	Enhancers	HepG2	liver
11	chr12:106689800-106691800	Enhancers	NHEK	skin
12	chr12:106690200-106693000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:106690200-106695400	Weak transcription	NHLF	lung
14	chr12:106690400-106693000	Weak transcription	NHDF-Ad	bronchial
15	chr12:106690600-106692800	Weak transcription	Placenta	Placenta
16	chr12:106690600-106693000	Weak transcription	Left Ventricle	heart
17	chr12:106690600-106694600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:106690600-106694600	Weak transcription	HSMM	muscle
19	chr12:106690600-106695000	Weak transcription	NH-A	brain
20	chr12:106690600-106695200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:106690600-106695400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:106690800-106693000	Weak transcription	Stomach Mucosa	stomach
23	chr12:106690800-106694600	Weak transcription	Osteobl	bone
24	chr12:106690800-106694800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:106690800-106695000	Weak transcription	HMEC	breast
26	chr12:106690800-106695400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:106690800-106695400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:106691000-106694600	Weak transcription	A549	lung
29	chr12:106691200-106691600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:106691200-106691600	Weak transcription	Hela-S3	cervix
31	chr12:106691200-106691800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr12:106691200-106691800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:106691200-106691800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:106691200-106692200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:106691200-106692200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:106691400-106691600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr12:106691400-106691800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr12:106691400-106691800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr12:106691400-106691800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:106691400-106691800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:106691400-106691800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:106691400-106691800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:106691400-106691800	Enhancers	GM12878-XiMat	blood
44	chr12:106691400-106692000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:106691400-106692000	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:106691400-106692000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:106691400-106692000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:106691400-106692000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:106691400-106692000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr12:106691400-106692200	Enhancers	Primary B cells from cord blood	blood

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