Variant report

Variant	rs833908
Chromosome Location	chr19:38481610-38481611
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38480879..38483750-chr19:38494788..38496320,2	MCF-7	breast:
2	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
3	chr19:38457253..38459371-chr19:38481407..38483076,2	MCF-7	breast:
4	chr19:38395223..38398524-chr19:38481213..38484062,6	MCF-7	breast:
5	chr19:38421711..38424524-chr19:38480296..38482978,4	MCF-7	breast:
6	chr19:38393241..38399415-chr19:38476540..38485383,15	MCF-7	breast:
7	chr19:38479835..38482339-chr19:38571881..38574395,2	MCF-7	breast:
8	chr19:38407792..38410171-chr19:38481203..38483917,2	MCF-7	breast:
9	chr19:38481055..38481656-chr19:38564723..38565599,2	MCF-7	breast:
10	chr19:38431713..38434433-chr19:38480033..38484198,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10853715	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1622543	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1643455	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1643456	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1643457	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1643459	0.83[EUR][1000 genomes]
rs1725501	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725503	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2694065	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57733318	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs705501	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs705502	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs833893	0.89[EUR][1000 genomes]
rs833894	0.92[EUR][1000 genomes]
rs833901	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs833902	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833903	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs833904	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833905	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833906	0.82[EUR][1000 genomes]
rs833907	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs833919	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs833920	0.88[EUR][1000 genomes]
rs833921	0.82[AMR][1000 genomes];0.92[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
4	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
6	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:38471400-38483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:38471400-38488600	Weak transcription	NHLF	lung
9	chr19:38472400-38493800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:38472800-38489600	Weak transcription	Fetal Kidney	kidney
11	chr19:38473200-38482000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:38473200-38482600	Weak transcription	HSMM	muscle
13	chr19:38473200-38488600	Weak transcription	HSMMtube	muscle
14	chr19:38474800-38513600	Weak transcription	Gastric	stomach
15	chr19:38475000-38488600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:38475600-38482000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:38475800-38488600	Weak transcription	Hela-S3	cervix
18	chr19:38476400-38482800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr19:38476400-38484800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:38476800-38481800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr19:38476800-38482800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr19:38476800-38482800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr19:38476800-38483800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr19:38477000-38482000	Weak transcription	Brain Substantia Nigra	brain
25	chr19:38477200-38483000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr19:38477200-38483800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr19:38477200-38488800	Weak transcription	Brain Anterior Caudate	brain
28	chr19:38477400-38481800	Weak transcription	Fetal Muscle Leg	muscle
29	chr19:38477400-38482000	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:38477400-38491800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:38477600-38482000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr19:38477600-38493800	Weak transcription	Thymus	Thymus
33	chr19:38478000-38483800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:38478000-38483800	Genic enhancers	A549	lung
35	chr19:38478200-38482400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr19:38478200-38482800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:38478200-38482800	Enhancers	Placenta	Placenta
38	chr19:38478200-38483800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:38478600-38483400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:38478800-38482400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38479200-38493800	Weak transcription	Colonic Mucosa	Colon
42	chr19:38479600-38482000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr19:38479600-38483000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:38479600-38485400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:38479800-38481800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:38479800-38482000	Weak transcription	Pancreas	Pancrea
47	chr19:38479800-38483400	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr19:38479800-38484800	Weak transcription	Primary T cells from cord blood	blood
49	chr19:38479800-38488600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:38479800-38489800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links