Variant report

Variant	rs12052117
Chromosome Location	chr19:19485105-19485106
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19483132..19485532-chr19:19492429..19494779,2	K562	blood:
2	chr19:19482280..19485550-chr19:19495820..19498182,3	K562	blood:
3	chr19:19483917..19485446-chr19:19554236..19556053,2	K562	blood:
4	chr19:19484050..19485886-chr19:19494826..19498217,3	K562	blood:
5	chr19:19482436..19485399-chr19:19514974..19516831,2	K562	blood:
6	chr19:19484073..19490340-chr19:19494015..19501154,14	MCF-7	breast:
7	chr19:19483095..19487397-chr19:19491404..19494790,5	K562	blood:
8	chr19:19472366..19475200-chr19:19483991..19486189,2	K562	blood:
9	chr19:19483123..19485621-chr19:19515015..19517445,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10408596	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10408875	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10415849	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10424702	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11668386	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11672355	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2285626	0.85[EUR][1000 genomes]
rs28720066	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56241616	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56273306	0.82[EUR][1000 genomes]
rs59148799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73002960	0.82[EUR][1000 genomes]
rs8182472	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19469800-19488400	Weak transcription	Gastric	stomach
2	chr19:19475800-19488000	Weak transcription	Small Intestine	intestine
3	chr19:19476200-19488200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:19476200-19488400	Weak transcription	Right Atrium	heart
5	chr19:19477800-19488400	Weak transcription	Fetal Muscle Leg	muscle
6	chr19:19477800-19488600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:19477800-19488600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:19478000-19488000	Weak transcription	Pancreas	Pancrea
9	chr19:19478000-19488200	Weak transcription	Spleen	Spleen
10	chr19:19478000-19488600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr19:19478800-19495800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:19482200-19485600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:19482200-19485600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:19482200-19485800	Weak transcription	NHEK	skin
15	chr19:19482200-19488200	Weak transcription	Right Ventricle	heart
16	chr19:19482200-19488200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:19482200-19488400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:19482400-19486200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:19482400-19488200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:19482600-19493200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr19:19483800-19485800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:19483800-19488200	Weak transcription	Left Ventricle	heart
23	chr19:19484000-19485600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:19484000-19488200	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:19484000-19488200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr19:19484000-19488200	Weak transcription	Fetal Intestine Large	intestine
27	chr19:19484000-19488400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:19484000-19488400	Weak transcription	HSMMtube	muscle
29	chr19:19484000-19488400	Weak transcription	NHDF-Ad	bronchial
30	chr19:19484000-19488400	Weak transcription	Osteobl	bone
31	chr19:19484000-19488600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr19:19484200-19485600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:19484200-19486000	Weak transcription	Hela-S3	cervix
34	chr19:19484200-19488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:19484200-19488200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:19484200-19488400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:19484200-19488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19484200-19488400	Weak transcription	Fetal Intestine Small	intestine
39	chr19:19484200-19488400	Weak transcription	A549	lung
40	chr19:19484200-19489000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr19:19484400-19485600	Weak transcription	GM12878-XiMat	blood
42	chr19:19484400-19485800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:19484400-19488000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr19:19484400-19488200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr19:19484400-19488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:19484400-19488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:19484400-19488400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:19484400-19488600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:19484400-19488600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:19484400-19488600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links