Variant report

Variant	rs12578367
Chromosome Location	chr12:47535643-47535644
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	CTCF	chr12:47535540-47535690	HepG2	liver:	n/a	n/a
2	CTCF	chr12:47535640-47535790	GM12871	blood:	n/a	n/a
3	TEAD4	chr12:47535274-47535646	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47533951..47536352-chr12:47547162..47551314,3	K562	blood:

Variant related genes	Relation type
ENSG00000258352	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10785658	0.83[CEU][hapmap]
rs10785659	0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs10881049	0.91[EUR][1000 genomes]
rs10881050	0.89[EUR][1000 genomes]
rs10881051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10881053	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183755	0.83[CEU][hapmap]
rs11183756	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612285	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371765	0.87[CEU][hapmap]
rs12578995	0.83[CEU][hapmap]
rs12579796	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12810420	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404812	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1404813	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404814	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404821	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525444	0.83[CEU][hapmap]
rs1525452	0.88[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs1581560	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917662	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917663	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949864	0.83[CEU][hapmap]
rs2091294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091295	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222609	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408714	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408715	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529959	0.84[EUR][1000 genomes]
rs4533118	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4544084	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598738	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768777	0.83[CEU][hapmap]
rs55651541	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7484989	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7958186	0.83[CEU][hapmap]
rs7963822	0.83[CEU][hapmap]
rs9634260	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3374724	chr12:47531385-47535683	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47505800-47538600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:47506200-47538400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:47508400-47545200	Weak transcription	HSMMtube	muscle
4	chr12:47517400-47538400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:47527000-47547800	Weak transcription	Ovary	ovary
6	chr12:47529600-47542600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:47531800-47536000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:47531800-47538000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:47533000-47536200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:47533200-47536200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:47533400-47541800	Weak transcription	Osteobl	bone
12	chr12:47533600-47536200	Weak transcription	Primary B cells from cord blood	blood
13	chr12:47533600-47536200	Strong transcription	Primary T cells from cord blood	blood
14	chr12:47533600-47538600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:47533600-47538600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:47533600-47542200	Weak transcription	Spleen	Spleen
17	chr12:47533800-47537600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:47533800-47542200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:47534200-47536800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:47534600-47535800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:47534600-47536000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:47534800-47536200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:47534800-47536400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr12:47535000-47535800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:47535000-47535800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:47535000-47536000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:47535000-47536000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:47535200-47535800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:47535200-47536000	Strong transcription	Aorta	Aorta
30	chr12:47535200-47536000	Strong transcription	Fetal Intestine Small	intestine
31	chr12:47535400-47535800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:47535400-47536000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:47535400-47536000	Strong transcription	Adipose Nuclei	Adipose
34	chr12:47535400-47536200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:47535600-47535800	Weak transcription	NHEK	skin
36	chr12:47535600-47536000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:47535600-47536000	Genic enhancers	HMEC	breast

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