Variant report

Variant	rs773644
Chromosome Location	chr12:56575742-56575743
allele	G/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	POLR2A	chr12:56575694-56575894	K562	blood:	n/a	n/a
2	POLR2A	chr12:56575721-56575970	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
2	chr12:56510353..56513279-chr12:56574826..56576600,2	MCF-7	breast:
3	chr12:56519914..56522865-chr12:56574395..56576124,2	MCF-7	breast:

Variant related genes	Relation type
SMARCC2	TF binding region
ENSG00000196465	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000092841	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10747762	0.81[AMR][1000 genomes]
rs11171774	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575218	1.00[MEX][hapmap]
rs1274501	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1619653	1.00[MEX][hapmap]
rs1689507	1.00[MEX][hapmap]
rs1689516	1.00[MEX][hapmap]
rs1701705	1.00[MEX][hapmap]
rs1995742	1.00[MEX][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes]
rs2066811	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2450101	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2450104	0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs2456445	1.00[MEX][hapmap]
rs2629449	0.91[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35382885	1.00[MEX][hapmap]
rs4759219	0.90[AMR][1000 genomes]
rs705706	1.00[MEX][hapmap]
rs7301099	0.82[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs773647	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs808896	1.00[MEX][hapmap]

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	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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	esv1792521	chr12:56575188-56587576	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56554000-56582000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56554200-56581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56555000-56579800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:56555000-56580800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr12:56555000-56580800	Strong transcription	Brain Anterior Caudate	brain
6	chr12:56555000-56581000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:56555200-56578800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:56555200-56580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:56555200-56580800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:56555400-56579000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:56555400-56580000	Strong transcription	Placenta	Placenta
12	chr12:56555400-56580600	Strong transcription	Thymus	Thymus
13	chr12:56555400-56580800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr12:56555400-56580800	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr12:56555400-56580800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:56555600-56576000	Strong transcription	Brain Cingulate Gyrus	brain
17	chr12:56555600-56580600	Strong transcription	Fetal Brain Female	brain
18	chr12:56555600-56580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:56555600-56580800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:56555600-56580800	Strong transcription	Liver	Liver
21	chr12:56555600-56580800	Strong transcription	Osteobl	bone
22	chr12:56555800-56580200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:56555800-56580600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:56555800-56580600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:56555800-56580800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:56555800-56580800	Strong transcription	Fetal Thymus	thymus
27	chr12:56555800-56580800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:56555800-56581000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:56556000-56578000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:56556000-56580800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:56556000-56580800	Strong transcription	Fetal Intestine Large	intestine
32	chr12:56556000-56581000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:56556000-56581000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr12:56556400-56580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:56556400-56580400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:56556600-56579800	Strong transcription	Dnd41	blood
37	chr12:56556600-56580600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:56556600-56580600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:56556600-56580800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:56556600-56581000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:56556600-56581000	Strong transcription	Fetal Stomach	stomach
42	chr12:56556800-56580800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:56556800-56581000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:56556800-56581000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:56556800-56581000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:56557200-56581000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:56557400-56580200	Strong transcription	Brain Germinal Matrix	brain
48	chr12:56557400-56580600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:56557400-56581200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:56557400-56581400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links