Variant report

Variant	rs1995742
Chromosome Location	chr12:56523976-56523977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56523790-56524870	K562	blood:	n/a	n/a
2	POLR2A	chr12:56523713-56524100	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56523930-56524882	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:56523905-56523988	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:
2	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
3	chr12:56433873..56442113-chr12:56515349..56524351,14	K562	blood:
4	chr12:56518236..56525779-chr12:56581707..56584752,14	MCF-7	breast:
5	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
6	chr12:56519569..56524417-chr12:56555136..56559386,7	MCF-7	breast:
7	chr12:56521888..56524004-chr12:56719736..56721397,2	K562	blood:
8	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:

No data

Variant related genes	Relation type
ESYT1	TF binding region
ENSG00000258317	TF binding region
ENSG00000139641	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000197728	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10747762	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11171774	1.00[AMR][1000 genomes]
rs1274501	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs1619653	1.00[MEX][hapmap]
rs1689507	1.00[MEX][hapmap]
rs1689516	1.00[MEX][hapmap]
rs1701705	1.00[MEX][hapmap]
rs2066811	0.90[AMR][1000 genomes]
rs2450101	0.91[AMR][1000 genomes]
rs2450104	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2456445	1.00[MEX][hapmap]
rs2629449	1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs35382885	1.00[MEX][hapmap]
rs4759219	1.00[AMR][1000 genomes]
rs705706	1.00[MEX][hapmap]
rs7301099	0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773644	1.00[MEX][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes]
rs773647	1.00[AMR][1000 genomes]
rs808896	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56520000-56524200	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:56521200-56524000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:56521200-56524000	Active TSS	NHDF-Ad	bronchial
4	chr12:56521600-56524000	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr12:56521600-56524200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:56521600-56524200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:56521800-56524000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:56522000-56524000	Flanking Active TSS	Dnd41	blood
9	chr12:56522000-56525000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:56522200-56524000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr12:56522200-56524000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:56522200-56524200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:56522200-56524200	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr12:56522200-56524200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr12:56523000-56524000	Flanking Active TSS	Fetal Thymus	thymus
16	chr12:56523200-56524000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr12:56523200-56524000	Flanking Active TSS	K562	blood
18	chr12:56523200-56524200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr12:56523200-56524200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:56523200-56524200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:56523200-56524200	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr12:56523200-56524400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
23	chr12:56523200-56524400	Flanking Active TSS	HSMM	muscle
24	chr12:56523200-56533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:56523400-56524000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:56523400-56524200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:56523400-56524200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:56523400-56524200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr12:56523400-56524400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr12:56523600-56524000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:56523600-56524000	Enhancers	Esophagus	oesophagus
32	chr12:56523600-56524000	Weak transcription	Gastric	stomach
33	chr12:56523600-56524200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:56523600-56524200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:56523600-56524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:56523600-56524200	Weak transcription	Aorta	Aorta
37	chr12:56523600-56524200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:56523600-56524200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:56523600-56524200	Active TSS	Rectal Smooth Muscle	rectum
40	chr12:56523600-56524400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:56523600-56524400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:56523600-56524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:56523600-56524400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr12:56523600-56524400	Weak transcription	A549	lung
45	chr12:56523600-56524600	Weak transcription	Brain Angular Gyrus	brain
46	chr12:56523600-56524600	Enhancers	Fetal Heart	heart
47	chr12:56523600-56524600	Weak transcription	Lung	lung
48	chr12:56523600-56524600	Weak transcription	Ovary	ovary
49	chr12:56523600-56524600	Enhancers	Pancreas	Pancrea
50	chr12:56523600-56524600	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links