Variant report

Variant	rs62208869
Chromosome Location	chr20:23612979-23612980
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	POLR2A	chr20:23611823-23615036	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
3	HEY1	chr20:23612370-23614357	HepG2	liver:	n/a	chr20:23612700-23612715
4	MBD4	chr20:23612711-23613700	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:23611815-23614265	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:23612891-23613098	HCT-116	colon:	n/a	n/a
7	POLR2A	chr20:23611753-23618814	HepG2	liver:	n/a	n/a
8	POLR2A	chr20:23610050-23614159	K562	blood:	n/a	n/a
9	POLR2A	chr20:23608691-23613357	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr20:23612950-23613032	K562	blood:	n/a	n/a
11	POLR2A	chr20:23611797-23614289	HepG2	liver:	n/a	n/a
12	POLR2A	chr20:23611874-23613520	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr20:23612583-23613459	HepG2	liver:	n/a	n/a
14	POLR2A	chr20:23612536-23614248	HepG2	liver:	n/a	n/a
15	POLR2A	chr20:23612904-23613129	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr20:23609430-23615030	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23332367..23335198-chr20:23611839..23614673,2	MCF-7	breast:
2	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270001	TF binding region
ENSG00000101439	Chromatin interaction
ENSG00000269407	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10485646	0.83[EUR][1000 genomes]
rs2983639	0.82[EUR][1000 genomes]
rs2983641	0.82[EUR][1000 genomes]
rs3004148	0.83[EUR][1000 genomes]
rs35701829	0.82[EUR][1000 genomes]
rs6036464	0.80[EUR][1000 genomes]
rs6106689	0.83[EUR][1000 genomes]
rs6106691	0.81[EUR][1000 genomes]
rs62207039	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62208864	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7265919	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73312653	0.82[EUR][1000 genomes]
rs8120131	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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 target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:23604000-23613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr20:23604000-23613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:23604000-23613400	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr20:23604200-23615000	Weak transcription	Brain Anterior Caudate	brain
11	chr20:23606600-23615200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:23606800-23616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:23607000-23615000	Weak transcription	Colon Smooth Muscle	Colon
15	chr20:23607600-23615400	Weak transcription	Fetal Kidney	kidney
16	chr20:23608200-23614400	Weak transcription	Thymus	Thymus
17	chr20:23608800-23613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr20:23609600-23615000	Weak transcription	HSMMtube	muscle
19	chr20:23609800-23616800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr20:23610000-23613800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr20:23610200-23617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr20:23610200-23617000	Weak transcription	K562	blood
24	chr20:23610400-23613400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr20:23610400-23613400	Weak transcription	Osteobl	bone
26	chr20:23610400-23613600	Weak transcription	HSMM	muscle
27	chr20:23610400-23613800	Weak transcription	Psoas Muscle	Psoas
28	chr20:23610400-23615400	Weak transcription	NHDF-Ad	bronchial
29	chr20:23610400-23616000	Weak transcription	Fetal Thymus	thymus
30	chr20:23610400-23616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr20:23610400-23616800	Weak transcription	NH-A	brain
32	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr20:23610600-23614400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:23610600-23616800	Weak transcription	Hela-S3	cervix
35	chr20:23610800-23615200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr20:23610800-23616800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr20:23610800-23617400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr20:23611000-23615600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr20:23611000-23616000	Strong transcription	Fetal Intestine Small	intestine
40	chr20:23611200-23613400	Weak transcription	HMEC	breast
41	chr20:23611200-23614000	Weak transcription	Stomach Mucosa	stomach
42	chr20:23611200-23615000	Weak transcription	Right Atrium	heart
43	chr20:23611200-23615800	Weak transcription	GM12878-XiMat	blood
44	chr20:23611400-23613000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr20:23611400-23613200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr20:23611400-23613400	Weak transcription	Ovary	ovary
47	chr20:23611400-23615600	Weak transcription	HUVEC	blood vessel
48	chr20:23611800-23613800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:23612000-23613200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr20:23612000-23613600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links