Variant report

Variant	rs62209207
Chromosome Location	chr20:13778744-13778745
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	GATA3	chr20:13778333-13778776	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13770594..13773511-chr20:13777159..13778904,2	MCF-7	breast:
2	chr20:13764873..13767036-chr20:13778027..13780324,2	MCF-7	breast:

Variant related genes	Relation type
NDUFAF5	TF binding region
ENSG00000101247	Chromatin interaction
ENSG00000089048	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13042637	0.94[ASN][1000 genomes]
rs1547920	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1999112	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031933	0.83[ASN][1000 genomes]
rs2209993	0.90[ASN][1000 genomes]
rs2209994	0.90[ASN][1000 genomes]
rs2423745	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2423749	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2423750	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2423753	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3180370	0.96[ASN][1000 genomes]
rs34449907	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34806363	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35361761	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35632254	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4813142	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814256	0.85[ASN][1000 genomes]
rs4814258	0.83[ASN][1000 genomes]
rs6033816	0.83[ASN][1000 genomes]
rs6033819	0.90[ASN][1000 genomes]
rs6033821	0.98[ASN][1000 genomes]
rs6042351	0.89[ASN][1000 genomes]
rs6042357	0.82[ASN][1000 genomes]
rs6042362	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074643	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074644	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079162	0.86[ASN][1000 genomes]
rs6079165	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079166	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079176	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079178	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079181	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079182	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110026	0.86[ASN][1000 genomes]
rs6110035	0.90[ASN][1000 genomes]
rs6134968	0.89[ASN][1000 genomes]
rs62209178	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68012295	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754796	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr20:13766400-13793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:13766400-13796800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:13766800-13781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:13767400-13792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:13767600-13789800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:13767600-13799600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:13767800-13799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr20:13767800-13800600	Weak transcription	Stomach Mucosa	stomach
9	chr20:13768000-13780600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:13768000-13781400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr20:13768000-13786000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr20:13768000-13794800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr20:13768000-13799800	Strong transcription	Fetal Thymus	thymus
14	chr20:13768200-13780000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:13768200-13780000	Strong transcription	Placenta	Placenta
16	chr20:13768200-13780400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:13768200-13799800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr20:13768200-13799800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr20:13768400-13799600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr20:13768600-13799600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr20:13768800-13780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:13768800-13786200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr20:13768800-13799600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr20:13769000-13781400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr20:13769000-13799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr20:13769200-13789800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr20:13769200-13799600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr20:13769400-13779800	Strong transcription	Osteobl	bone
29	chr20:13769400-13786000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:13769400-13799400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr20:13769400-13802000	Strong transcription	A549	lung
32	chr20:13769600-13780800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr20:13769600-13780800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:13769600-13799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr20:13769800-13779200	Strong transcription	Adipose Nuclei	Adipose
36	chr20:13769800-13785600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr20:13769800-13785800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr20:13769800-13786400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr20:13769800-13786400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr20:13769800-13787200	Strong transcription	Fetal Intestine Large	intestine
41	chr20:13769800-13788600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr20:13770000-13781000	Strong transcription	Fetal Brain Female	brain
43	chr20:13770000-13787000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr20:13770200-13779800	Strong transcription	HMEC	breast
45	chr20:13770200-13781400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr20:13770200-13799600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr20:13770400-13785600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr20:13770600-13780000	Strong transcription	NHDF-Ad	bronchial
49	chr20:13770600-13784200	Strong transcription	GM12878-XiMat	blood
50	chr20:13770600-13799400	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links