Variant report

Variant	rs17315467
Chromosome Location	chr12:25056665-25056666
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	RUNX3	chr12:25055124-25057096	GM12878	blood:	n/a	n/a
2	FOXM1	chr12:25056479-25057036	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:25053871-25057036	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:25054579-25057018	HUVEC	blood vessel:	n/a	n/a
5	NFIC	chr12:25056627-25057109	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:25055514-25057040	PBDE	blood:	n/a	n/a
7	POLR2A	chr12:25054640-25056880	H1-hESC	embryonic stem cell:	n/a	n/a
8	MTA3	chr12:25055905-25056910	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:25055720-25056969	HUVEC	blood vessel:	n/a	n/a
10	RUNX3	chr12:25056100-25057017	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:25055180-25056979	K562	blood:	n/a	n/a
12	GATA1	chr12:25056660-25057164	PBDE	blood:	n/a	chr12:25056962-25056978 chr12:25056962-25056978
13	POLR2A	chr12:25053857-25056880	HUVEC	blood vessel:	n/a	n/a
14	MTA3	chr12:25055364-25056737	GM12878	blood:	n/a	n/a
15	PML	chr12:25053730-25057048	GM12878	blood:	n/a	chr12:25054062-25054071

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25056075..25057802-chr12:25059438..25060950,2	K562	blood:

Variant related genes	Relation type
BCAT1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17315488	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2291895	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60558352	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs954200	0.85[MEX][hapmap]
rs9804807	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9804952	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1053309	chr12:24770995-25078227	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
8	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv1045302	chr12:24921100-25078227	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
17	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1054863	chr12:24941350-25078227	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
20	nsv541426	chr12:24941350-25078227	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
21	nsv1051968	chr12:24941350-25138118	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	nsv541427	chr12:24941350-25138118	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
24	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
25	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25031200-25063600	Weak transcription	HepG2	liver
2	chr12:25053200-25057200	Flanking Active TSS	HUVEC	blood vessel
3	chr12:25053600-25057000	Active TSS	Brain Anterior Caudate	brain
4	chr12:25054000-25056800	Bivalent/Poised TSS	Fetal Kidney	kidney
5	chr12:25054000-25057200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:25054200-25057000	Active TSS	Brain Substantia Nigra	brain
7	chr12:25054600-25056800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:25054600-25056800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr12:25054600-25057200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:25054800-25056800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:25054800-25057200	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr12:25054800-25057400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:25055000-25056800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
14	chr12:25055000-25057000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr12:25055000-25057000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr12:25055000-25057000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
17	chr12:25055000-25057000	Active TSS	Brain Cingulate Gyrus	brain
18	chr12:25055200-25056800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr12:25055200-25056800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
20	chr12:25055200-25056800	Active TSS	Right Atrium	heart
21	chr12:25055200-25057000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr12:25055400-25056800	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr12:25055400-25056800	Active TSS	Rectal Smooth Muscle	rectum
24	chr12:25055600-25056800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
25	chr12:25055600-25056800	ZNF genes & repeats	K562	blood
26	chr12:25055800-25056800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:25056000-25056800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:25056200-25056800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:25056200-25056800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:25056200-25056800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:25056200-25056800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:25056200-25056800	Bivalent/Poised TSS	Fetal Lung	lung
33	chr12:25056200-25056800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr12:25056200-25056800	Enhancers	Spleen	Spleen
35	chr12:25056200-25056800	Flanking Active TSS	NHLF	lung
36	chr12:25056200-25057000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:25056200-25057000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:25056200-25057000	Flanking Active TSS	GM12878-XiMat	blood
39	chr12:25056200-25057200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr12:25056200-25057200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:25056200-25062400	Weak transcription	Pancreas	Pancrea
42	chr12:25056200-25064400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:25056400-25056800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
44	chr12:25056400-25056800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
45	chr12:25056400-25056800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:25056400-25056800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:25056400-25056800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:25056400-25056800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
49	chr12:25056400-25056800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
50	chr12:25056400-25056800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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