Variant report

Variant	rs4802923
Chromosome Location	chr19:52856703-52856704
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1961205	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2251559	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560979	0.90[EUR][1000 genomes]
rs321940	0.90[EUR][1000 genomes]
rs321948	0.90[EUR][1000 genomes]
rs321949	0.91[EUR][1000 genomes]
rs3745098	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4802924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7246724	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52857400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:52840600-52856800	Weak transcription	HSMM	muscle
4	chr19:52840600-52858800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:52840800-52857000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:52840800-52857000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:52841400-52857000	Weak transcription	Right Ventricle	heart
9	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
11	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:52848800-52858400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:52849000-52857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
17	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:52851000-52857200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:52851200-52856800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:52851200-52859000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
25	chr19:52851800-52857000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr19:52852000-52858200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:52852200-52857000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:52852200-52858000	Weak transcription	Fetal Kidney	kidney
29	chr19:52852400-52858400	Weak transcription	Colonic Mucosa	Colon
30	chr19:52852400-52858800	Weak transcription	Fetal Brain Male	brain
31	chr19:52852600-52856800	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:52852600-52857000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:52852600-52857000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:52852600-52857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:52852600-52857200	Weak transcription	Osteobl	bone
36	chr19:52852800-52856800	Weak transcription	Primary T cells from cord blood	blood
37	chr19:52852800-52857000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:52852800-52857000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:52853400-52856800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:52853400-52857200	Weak transcription	HSMMtube	muscle
41	chr19:52853400-52858400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr19:52853600-52857000	Weak transcription	Primary B cells from cord blood	blood
43	chr19:52853600-52857000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:52853600-52858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:52853800-52856800	Weak transcription	Fetal Lung	lung
46	chr19:52854000-52857400	Weak transcription	Brain Substantia Nigra	brain
47	chr19:52854200-52857000	Weak transcription	Placenta	Placenta
48	chr19:52854200-52860400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:52854600-52861200	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:52854800-52859400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links