Variant report

Variant	rs2617160
Chromosome Location	chr12:10545597-10545598
allele	A/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	SPI1	chr12:10545363-10545610	GM12878	blood:	n/a	n/a
2	ATF2	chr12:10544776-10545621	GM12878	blood:	n/a	n/a
3	MAX	chr12:10545002-10545598	Hela-S3	cervix:	n/a	n/a
4	FOS	chr12:10544703-10545920	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr12:10545012-10545750	MCF10A-Er-Src	breast:	n/a	n/a
6	RUNX3	chr12:10544883-10545644	GM12878	blood:	n/a	n/a
7	SP1	chr12:10544831-10545694	HCT-116	colon:	n/a	n/a
8	TBP	chr12:10544509-10545707	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr12:10545039-10545629	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr12:10544879-10545646	GM12878	blood:	n/a	chr12:10545485-10545499
11	FOS	chr12:10544999-10545686	MCF10A-Er-Src	breast:	n/a	n/a
12	MTA3	chr12:10544931-10545600	GM12878	blood:	n/a	n/a
13	FOSL1	chr12:10544990-10545769	HCT-116	colon:	n/a	n/a
14	MAFK	chr12:10545372-10545636	HepG2	liver:	n/a	chr12:10545496-10545507 chr12:10545495-10545510
15	STAT3	chr12:10545040-10545718	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr12:10545059-10545675	MCF10A-Er-Src	breast:	n/a	n/a
17	PML	chr12:10544773-10545658	GM12878	blood:	n/a	n/a
18	TCF12	chr12:10544859-10545680	A549	lung:	n/a	n/a
19	FOXM1	chr12:10544853-10545699	GM12878	blood:	n/a	n/a
20	FOS	chr12:10544735-10545683	MCF10A-Er-Src	breast:	n/a	n/a
21	MYC	chr12:10545000-10545638	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr12:10544931-10545888	MCF10A-Er-Src	breast:	n/a	n/a
23	RUNX3	chr12:10544768-10545745	GM12878	blood:	n/a	n/a
24	STAT3	chr12:10545051-10545597	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr12:10544936-10545623	GM12878	blood:	n/a	chr12:10545485-10545499
26	NFIC	chr12:10544773-10545757	GM12878	blood:	n/a	chr12:10545713-10545729
27	NFIC	chr12:10544735-10545701	ECC-1	luminal epithelium:	n/a	n/a
28	NFIC	chr12:10544834-10545605	ECC-1	luminal epithelium:	n/a	n/a
29	MAFK	chr12:10544770-10545649	Hela-S3	cervix:	n/a	chr12:10545496-10545507 chr12:10545495-10545510

Variant related genes	Relation type
KLRK1	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1049172	1.00[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1049174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10772275	0.85[ASN][1000 genomes]
rs11053781	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11053801	0.95[CEU][hapmap]
rs11053802	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs11053803	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1351111	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1351112	0.87[ASN][1000 genomes]
rs1351113	1.00[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1600128	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841957	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1841958	0.95[CEU][hapmap]
rs1904123	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967432	0.95[CHB][hapmap]
rs1983526	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2086098	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2086099	0.90[EUR][1000 genomes]
rs2250877	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617149	1.00[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs2617150	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2617170	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617171	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682472	0.95[CHB][hapmap]
rs2733841	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733851	0.90[EUR][1000 genomes]
rs2733852	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2734414	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2734440	0.95[CHB][hapmap];0.82[CHD][hapmap]
rs2734565	0.95[CEU][hapmap]
rs4492900	0.85[CHB][hapmap]
rs7485868	0.90[ASN][1000 genomes]
rs7975996	0.89[EUR][1000 genomes]
rs7978962	0.89[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2617160	KLRC3	cis	multi-tissue	Pritchard
rs2617160	KLRK1	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 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	chr12:10543800-10547600	Enhancers	Hela-S3	cervix
7	chr12:10543800-10547800	Enhancers	Primary B cells from cord blood	blood
8	chr12:10544200-10548200	Enhancers	Primary T cells from cord blood	blood
9	chr12:10544400-10545800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:10544400-10545800	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:10544400-10545800	Enhancers	Osteobl	bone
12	chr12:10544400-10546000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:10544400-10546200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:10544400-10546200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:10544400-10547800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr12:10544400-10548200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:10544400-10550800	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:10544600-10545600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:10544600-10545800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:10544600-10545800	Enhancers	HSMM	muscle
21	chr12:10544600-10548800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:10544600-10549000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:10544800-10545800	Enhancers	NHDF-Ad	bronchial
24	chr12:10544800-10546400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:10544800-10547800	Weak transcription	Adipose Nuclei	Adipose
26	chr12:10545000-10545600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr12:10545000-10545600	Enhancers	Esophagus	oesophagus
28	chr12:10545000-10545800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:10545200-10545600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:10545200-10545600	Flanking Active TSS	GM12878-XiMat	blood
31	chr12:10545200-10545800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:10545200-10547800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr12:10545200-10548000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:10545400-10545600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr12:10545400-10545800	Enhancers	A549	lung
36	chr12:10545400-10546000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:10545400-10546000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr12:10545400-10546400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:10545400-10546800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr12:10545400-10547000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:10545400-10547000	Weak transcription	Fetal Thymus	thymus
42	chr12:10545400-10548000	Weak transcription	Fetal Lung	lung
43	chr12:10545400-10548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:10545400-10548000	Weak transcription	HSMMtube	muscle
45	chr12:10545400-10548200	Enhancers	NHEK	skin
46	chr12:10545400-10549000	Enhancers	HMEC	breast

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