Variant report

Variant	rs16985269
Chromosome Location	chr20:23344775-23344776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23341279-23355011	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:23344769-23344814	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:23344712-23344818	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr20:23341069-23355530	K562	blood:	n/a	n/a
5	POLR2A	chr20:23340935-23347328	IMR90	lung:	n/a	n/a
6	POLR2A	chr20:23341111-23344823	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:38978307..38979883-chr20:23342389..23345213,2	MCF-7	breast:
2	chr20:23342672..23344892-chr20:23400555..23402881,3	MCF-7	breast:
3	chr20:23344681..23346860-chr20:23360081..23363046,2	MCF-7	breast:
4	chr20:23338809..23345308-chr20:23399768..23403114,12	K562	blood:

No data

Variant related genes	Relation type
GZF1	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000201728	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11087426	1.00[AMR][1000 genomes]
rs12106211	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16985333	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16985354	0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs16985360	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1891687	1.00[MEX][hapmap]
rs6036383	1.00[MEX][hapmap]
rs6048855	1.00[MEX][hapmap]
rs6083085	0.81[LWK][hapmap]
rs6114156	1.00[MEX][hapmap]
rs6132617	1.00[YRI][hapmap]
rs7260937	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7272812	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs766068	1.00[MEX][hapmap]
rs8123761	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23342400-23352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23343400-23344800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr20:23343400-23345000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr20:23343400-23345000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr20:23343600-23344800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:23343600-23345200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr20:23343800-23345000	Flanking Active TSS	GM12878-XiMat	blood
8	chr20:23344000-23344800	Enhancers	Primary T cells from cord blood	blood
9	chr20:23344000-23344800	Enhancers	Brain Substantia Nigra	brain
10	chr20:23344000-23344800	Enhancers	Stomach Mucosa	stomach
11	chr20:23344000-23345200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr20:23344000-23345200	Enhancers	Adipose Nuclei	Adipose
13	chr20:23344000-23345200	Enhancers	Right Atrium	heart
14	chr20:23344000-23345400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr20:23344000-23345400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr20:23344000-23346000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr20:23344000-23347600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr20:23344200-23344800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr20:23344200-23344800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr20:23344200-23344800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr20:23344200-23344800	Enhancers	HUVEC	blood vessel
23	chr20:23344200-23344800	Enhancers	NH-A	brain
24	chr20:23344200-23345000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr20:23344200-23345000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr20:23344200-23345000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr20:23344200-23345000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr20:23344200-23345000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:23344200-23345000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr20:23344200-23345000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr20:23344200-23345000	Weak transcription	Liver	Liver
32	chr20:23344200-23345000	Enhancers	Brain Cingulate Gyrus	brain
33	chr20:23344200-23345000	Weak transcription	Fetal Thymus	thymus
34	chr20:23344200-23345000	Weak transcription	Gastric	stomach
35	chr20:23344200-23345000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr20:23344200-23345000	Weak transcription	Thymus	Thymus
37	chr20:23344200-23345200	Weak transcription	Aorta	Aorta
38	chr20:23344200-23345200	Weak transcription	Brain Germinal Matrix	brain
39	chr20:23344200-23345400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr20:23344200-23345800	Weak transcription	Ovary	ovary
41	chr20:23344200-23346000	Weak transcription	Fetal Brain Male	brain
42	chr20:23344200-23346600	Genic enhancers	Spleen	Spleen
43	chr20:23344400-23344800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr20:23344400-23344800	Enhancers	HMEC	breast
45	chr20:23344400-23344800	Enhancers	NHLF	lung
46	chr20:23344400-23345000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:23344400-23345000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr20:23344400-23345000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr20:23344400-23345000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr20:23344400-23345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links