Variant report

Variant	rs2305390
Chromosome Location	chr12:57906282-57906283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57906229-57906885	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:57905370-57907700	U87	brain:	n/a	n/a
3	POLR2A	chr12:57905482-57906989	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:57906236-57906950	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:57904506-57914962	K562	blood:	n/a	n/a
6	POLR2A	chr12:57906257-57906956	HCT-116	colon:	n/a	n/a
7	POLR2A	chr12:57904889-57907759	U87	brain:	n/a	n/a
8	POLR2A	chr12:57906259-57906915	K562	blood:	n/a	n/a
9	POLR2A	chr12:57904883-57907734	U87	brain:	n/a	n/a
10	POLR2A	chr12:57905329-57906975	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:57905715-57906857	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr12:57906072-57906356	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:57905315-57908003	U87	brain:	n/a	n/a
14	POLR2A	chr12:57906251-57907670	HCT-116	colon:	n/a	n/a
15	POLR2A	chr12:57905360-57907442	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:57905765-57907030	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:57905082-57907629	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:57905814-57906573	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57879207..57888227-chr12:57906247..57918451,36	K562	blood:
2	chr12:57882180..57883907-chr12:57905478..57906996,2	MCF-7	breast:
3	chr12:57896366..57901111-chr12:57901647..57907518,8	K562	blood:
4	chr12:57879869..57888452-chr12:57905809..57918310,36	K562	blood:

No data

Variant related genes	Relation type
MARS	TF binding region
RN7SL312P	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000123329	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10437954	1.00[JPT][hapmap]
rs2229300	1.00[JPT][hapmap]
rs2277319	1.00[JPT][hapmap]
rs2278846	0.92[ASN][1000 genomes]
rs2290297	1.00[ASN][1000 genomes]
rs3802987	0.92[ASN][1000 genomes]
rs775244	0.87[CHD][hapmap];1.00[JPT][hapmap]

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	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	106 gene(s)	inside rSNPs	diseases
3	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
15	esv3419248	chr12:57904485-57908083	Strong transcription Weak transcription	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
2	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
3	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
4	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
5	chr12:57892800-57908600	Weak transcription	Stomach Mucosa	stomach
6	chr12:57899600-57906400	Weak transcription	Small Intestine	intestine
7	chr12:57900600-57912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:57900600-57912800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:57901600-57910600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:57901600-57911000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:57901600-57911800	Strong transcription	Lung	lung
12	chr12:57901800-57906800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:57901800-57911600	Strong transcription	Thymus	Thymus
14	chr12:57901800-57911800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:57901800-57911800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:57902000-57912400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr12:57902200-57909800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:57902200-57910000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:57902200-57910600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:57902200-57911600	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:57902200-57912000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:57902200-57912000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:57902200-57912400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr12:57902400-57910400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:57902400-57910800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:57902400-57910800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:57902400-57911000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:57902400-57911200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:57902400-57911600	Strong transcription	Fetal Thymus	thymus
30	chr12:57902400-57911800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:57902400-57911800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:57902400-57912000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:57902400-57912000	Strong transcription	Primary B cells from cord blood	blood
34	chr12:57902400-57912000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:57902400-57912000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:57902400-57912000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:57902400-57912200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:57902400-57912200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:57902400-57912400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:57902400-57912800	Strong transcription	Fetal Brain Female	brain
41	chr12:57902600-57906800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:57902600-57910400	Strong transcription	Dnd41	blood
43	chr12:57902600-57910600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:57902600-57910600	Strong transcription	Liver	Liver
45	chr12:57902600-57910800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:57902600-57911000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:57902600-57911000	Strong transcription	Adipose Nuclei	Adipose
48	chr12:57902600-57911200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr12:57902600-57911200	Strong transcription	HSMM	muscle
50	chr12:57902600-57911600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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