Variant report

Variant	rs7954052
Chromosome Location	chr12:10545057-10545058
allele	C/T
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	TCF12	chr12:10545033-10545335	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:10544914-10545427	PANC-1	pancreas:	n/a	n/a
3	ATF2	chr12:10544776-10545621	GM12878	blood:	n/a	n/a
4	GTF2F1	chr12:10544908-10545594	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:10545030-10545448	HL-60	blood:	n/a	n/a
6	RFX5	chr12:10544425-10545540	Hela-S3	cervix:	n/a	chr12:10545028-10545036
7	MAX	chr12:10545002-10545598	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr12:10544979-10545520	ECC-1	luminal epithelium:	n/a	chr12:10545280-10545293 chr12:10545280-10545291 chr12:10545280-10545291
9	FOS	chr12:10544703-10545920	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr12:10544919-10545095	MCF10A-Er-Src	breast:	n/a	n/a
11	TAF1	chr12:10544888-10545331	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr12:10544977-10545404	ECC-1	luminal epithelium:	n/a	chr12:10545280-10545293 chr12:10545280-10545291 chr12:10545280-10545291
13	ESR1	chr12:10544939-10545349	ECC-1	luminal epithelium:	n/a	n/a
14	CEBPB	chr12:10544897-10545572	HCT-116	colon:	n/a	chr12:10545280-10545293 chr12:10545280-10545291 chr12:10544957-10544968 chr12:10545280-10545291
15	POLR2A	chr12:10544997-10545373	HCT-116	colon:	n/a	n/a
16	MYC	chr12:10545012-10545750	MCF10A-Er-Src	breast:	n/a	n/a
17	RUNX3	chr12:10544883-10545644	GM12878	blood:	n/a	n/a
18	FOXA2	chr12:10545008-10545399	A549	lung:	n/a	n/a
19	SMC3	chr12:10544961-10545485	Hela-S3	cervix:	n/a	n/a
20	SP1	chr12:10544831-10545694	HCT-116	colon:	n/a	n/a
21	POLR2A	chr12:10544928-10545269	Hela-S3	cervix:	n/a	n/a
22	TBP	chr12:10544509-10545707	Hela-S3	cervix:	n/a	n/a
23	POU2F2	chr12:10545008-10545331	GM12891	blood:	n/a	n/a
24	BCL11A	chr12:10544909-10545281	GM12878	blood:	n/a	n/a
25	TEAD4	chr12:10544901-10545464	ECC-1	luminal epithelium:	n/a	n/a
26	FOXA1	chr12:10544999-10545309	T-47D	breast:	n/a	n/a
27	CHD2	chr12:10545000-10545449	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr12:10545019-10545516	A549	lung:	n/a	chr12:10545280-10545293 chr12:10545280-10545291 chr12:10545280-10545291
29	TCF7L2	chr12:10544903-10545510	Hela-S3	cervix:	n/a	n/a
30	CHD2	chr12:10544942-10545355	GM12878	blood:	n/a	n/a
31	STAT3	chr12:10545039-10545629	MCF10A-Er-Src	breast:	n/a	n/a
32	EP300	chr12:10544870-10545554	ECC-1	luminal epithelium:	n/a	chr12:10545485-10545499
33	YY1	chr12:10545055-10545304	GM12878	blood:	n/a	n/a
34	PRDM1	chr12:10544899-10545495	Hela-S3	cervix:	n/a	n/a
35	NR3C1	chr12:10545041-10545441	A549	lung:	n/a	n/a
36	CEBPB	chr12:10544944-10545549	Hela-S3	cervix:	n/a	chr12:10545280-10545293 chr12:10545280-10545291 chr12:10544957-10544968 chr12:10545280-10545291
37	POLR2A	chr12:10544970-10545289	HCT-116	colon:	n/a	n/a
38	MAX	chr12:10544983-10545571	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr12:10544711-10545499	Hela-S3	cervix:	n/a	n/a
40	BRCA1	chr12:10544899-10545539	Hela-S3	cervix:	n/a	n/a
41	EP300	chr12:10544879-10545646	GM12878	blood:	n/a	chr12:10545485-10545499
42	FOS	chr12:10544999-10545686	MCF10A-Er-Src	breast:	n/a	n/a
43	TCF12	chr12:10544995-10545262	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:10544864-10545269	GM12891	blood:	n/a	n/a
45	ESR1	chr12:10544895-10545378	ECC-1	luminal epithelium:	n/a	n/a
46	TEAD4	chr12:10544872-10545523	ECC-1	luminal epithelium:	n/a	n/a
47	JUND	chr12:10544961-10545595	HCT-116	colon:	n/a	n/a
48	BCLAF1	chr12:10544936-10545515	GM12878	blood:	n/a	chr12:10545490-10545499
49	POLR2A	chr12:10544408-10545504	Hela-S3	cervix:	n/a	n/a
50	STAT3	chr12:10544355-10545464	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
KLRK1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11832581	0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs11834973	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11836503	0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2061754	0.82[AFR][1000 genomes]
rs55670136	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56056709	0.91[AFR][1000 genomes]
rs57449593	0.93[AFR][1000 genomes]
rs57563883	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58737658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60077215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60106440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73256263	0.85[AMR][1000 genomes]
rs73256265	0.85[AMR][1000 genomes]
rs73256280	0.85[AMR][1000 genomes]
rs73256283	0.85[AMR][1000 genomes]
rs73256286	0.85[AMR][1000 genomes]
rs73256289	0.85[AMR][1000 genomes]
rs73256293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73258205	0.85[AMR][1000 genomes]
rs74060380	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription 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 target site	13 gene(s)	inside rSNPs	diseases
5	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv8914	chr12:10532300-10662676	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv557456	chr12:10532326-10698255	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv898764	chr12:10537269-10698255	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv898765	chr12:10537269-10701992	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv898766	chr12:10537269-10722585	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv430461	chr12:10539815-10554033	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10519600-10547800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:10525400-10547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10534800-10548800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:10542000-10549200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:10542800-10547800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:10543000-10545400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:10543800-10547600	Enhancers	Hela-S3	cervix
8	chr12:10543800-10547800	Enhancers	Primary B cells from cord blood	blood
9	chr12:10544200-10548200	Enhancers	Primary T cells from cord blood	blood
10	chr12:10544400-10545200	Enhancers	GM12878-XiMat	blood
11	chr12:10544400-10545400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr12:10544400-10545800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:10544400-10545800	Enhancers	Primary hematopoietic stem cells	blood
14	chr12:10544400-10545800	Enhancers	Osteobl	bone
15	chr12:10544400-10546000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:10544400-10546200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:10544400-10546200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:10544400-10547800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:10544400-10548200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:10544400-10550800	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:10544600-10545200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr12:10544600-10545400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr12:10544600-10545400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr12:10544600-10545400	Flanking Active TSS	NHEK	skin
25	chr12:10544600-10545600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:10544600-10545800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:10544600-10545800	Enhancers	HSMM	muscle
28	chr12:10544600-10548800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:10544600-10549000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:10544800-10545400	Enhancers	Fetal Lung	lung
31	chr12:10544800-10545400	Flanking Active TSS	HMEC	breast
32	chr12:10544800-10545800	Enhancers	NHDF-Ad	bronchial
33	chr12:10544800-10546400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:10544800-10547800	Weak transcription	Adipose Nuclei	Adipose
35	chr12:10545000-10545200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:10545000-10545200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:10545000-10545200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:10545000-10545200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:10545000-10545200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:10545000-10545400	Enhancers	Fetal Thymus	thymus
41	chr12:10545000-10545400	Flanking Active TSS	A549	lung
42	chr12:10545000-10545400	Enhancers	HSMMtube	muscle
43	chr12:10545000-10545600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr12:10545000-10545600	Enhancers	Esophagus	oesophagus
45	chr12:10545000-10545800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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