Variant report

Variant	rs554170690
Chromosome Location	chr12:25055827-25055828
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	RUNX3	chr12:25055124-25057096	GM12878	blood:	n/a	n/a
2	CREB1	chr12:25055602-25056299	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr12:25054870-25056625	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr12:25054726-25056546	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr12:25053714-25056156	H1-neurons	neurons:	n/a	chr12:25055556-25055566 chr12:25055616-25055629 chr12:25056057-25056070
6	POLR2A	chr12:25055472-25056573	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:25053871-25057036	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr12:25054579-25057018	HUVEC	blood vessel:	n/a	n/a
9	YY1	chr12:25055548-25055842	GM12878	blood:	n/a	n/a
10	MAX	chr12:25055464-25056270	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD1	chr12:25055747-25056229	H1-hESC	embryonic stem cell:	n/a	chr12:25056219-25056226
12	POLR2A	chr12:25055523-25056233	GM12878	blood:	n/a	n/a
13	RCOR1	chr12:25055622-25056367	GM12878	blood:	n/a	n/a
14	CTCF	chr12:25055800-25055950	GM12871	blood:	n/a	n/a
15	POLR2A	chr12:25055514-25057040	PBDE	blood:	n/a	n/a
16	FOXM1	chr12:25055561-25056052	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:25054640-25056880	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr12:25055691-25056493	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF3	chr12:25055718-25056091	GM12878	blood:	n/a	n/a
20	CCNT2	chr12:25055572-25056008	K562	blood:	n/a	n/a
21	YY1	chr12:25055457-25056492	H1-hESC	embryonic stem cell:	n/a	chr12:25055894-25055905
22	POLR2A	chr12:25055456-25056231	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr12:25055594-25056350	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:25054877-25056537	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr12:25054784-25056574	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr12:25055232-25056072	GM12878	blood:	n/a	n/a
27	TAF1	chr12:25055824-25056213	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:25055375-25056539	U87	brain:	n/a	n/a
29	POLR2A	chr12:25055485-25056186	HUVEC	blood vessel:	n/a	n/a
30	RUNX3	chr12:25055157-25056088	GM12878	blood:	n/a	n/a
31	GTF2F1	chr12:25055815-25056081	H1-hESC	embryonic stem cell:	n/a	n/a
32	STAT5A	chr12:25055784-25056396	GM12878	blood:	n/a	chr12:25055981-25055992
33	POLR2A	chr12:25055523-25056223	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:25055117-25056633	GM12878	blood:	n/a	n/a
35	TAF1	chr12:25055698-25056094	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:25055550-25056161	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr12:25055720-25056969	HUVEC	blood vessel:	n/a	n/a
38	ZNF143	chr12:25055612-25056186	H1-hESC	embryonic stem cell:	n/a	chr12:25055928-25055946
39	PAX5	chr12:25055568-25056042	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:25055433-25056539	U87	brain:	n/a	n/a
41	MXI1	chr12:25055736-25055912	GM12878	blood:	n/a	n/a
42	E2F6	chr12:25054878-25056273	H1-hESC	embryonic stem cell:	n/a	chr12:25056219-25056226
43	POLR2A	chr12:25055031-25056500	U87	brain:	n/a	n/a
44	MTA3	chr12:25055361-25055843	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:25055180-25056979	K562	blood:	n/a	n/a
46	POLR2A	chr12:25055632-25056257	H1-hESC	embryonic stem cell:	n/a	n/a
47	PAX5	chr12:25055769-25056131	GM12892	blood:	n/a	n/a
48	FOXM1	chr12:25055410-25056111	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:25055031-25056449	U87	brain:	n/a	n/a
50	POLR2A	chr12:25053857-25056880	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
BCAT1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 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
26	nsv520878	chr12:25054891-25056065	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 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	chr12:25054000-25056000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:25054000-25056400	Active TSS	Brain Angular Gyrus	brain
6	chr12:25054000-25056600	Active TSS	Fetal Brain Female	brain
7	chr12:25054000-25056800	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr12:25054000-25057200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:25054200-25056400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr12:25054200-25056600	Active TSS	Brain Hippocampus Middle	brain
11	chr12:25054200-25057000	Active TSS	Brain Substantia Nigra	brain
12	chr12:25054600-25056400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:25054600-25056800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:25054600-25056800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr12:25054600-25057200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:25054800-25056000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:25054800-25056000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:25054800-25056000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr12:25054800-25056000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:25054800-25056200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:25054800-25056200	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:25054800-25056200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:25054800-25056200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:25054800-25056400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:25054800-25056400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:25054800-25056400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:25054800-25056400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:25054800-25056600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:25054800-25056600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:25054800-25056800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr12:25054800-25057200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr12:25054800-25057400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:25055000-25056000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
34	chr12:25055000-25056200	Active TSS	H1 Cell Line	embryonic stem cell
35	chr12:25055000-25056200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:25055000-25056400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
37	chr12:25055000-25056600	Active TSS	Fetal Brain Male	brain
38	chr12:25055000-25056800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
39	chr12:25055000-25057000	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr12:25055000-25057000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr12:25055000-25057000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
42	chr12:25055000-25057000	Active TSS	Brain Cingulate Gyrus	brain
43	chr12:25055200-25056200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:25055200-25056200	Active TSS	Fetal Lung	lung
45	chr12:25055200-25056400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:25055200-25056400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:25055200-25056400	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr12:25055200-25056400	Active TSS	HSMM	muscle
49	chr12:25055200-25056600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:25055200-25056600	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links