Variant report

Variant	rs1961205
Chromosome Location	chr19:52856955-52856956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs2251559	0.92[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2560979	0.87[EUR][1000 genomes]
rs321940	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs321948	1.00[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs321949	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs3745098	0.89[GIH][hapmap]
rs4802923	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4802924	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7246724	0.86[EUR][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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1961205	SYT5	cis	cerebellum	SCAN
rs1961205	LILRB2	cis	cerebellum	SCAN
rs1961205	GALP	cis	cerebellum	SCAN
rs1961205	PYGL	trans	parietal	SCAN
rs1961205	U2AF2	cis	parietal	SCAN

Chromatin state (count:89 , 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	chr19:52840600-52858800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:52840800-52857000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:52840800-52857000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:52841400-52857000	Weak transcription	Right Ventricle	heart
8	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
10	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:52848800-52858400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:52849000-52857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
16	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:52851000-52857200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:52851200-52859000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:52851600-52864200	Strong transcription	Brain Germinal Matrix	brain
23	chr19:52851800-52857000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr19:52852000-52858200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:52852200-52857000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:52852200-52858000	Weak transcription	Fetal Kidney	kidney
27	chr19:52852400-52858400	Weak transcription	Colonic Mucosa	Colon
28	chr19:52852400-52858800	Weak transcription	Fetal Brain Male	brain
29	chr19:52852600-52857000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr19:52852600-52857000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:52852600-52857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:52852600-52857200	Weak transcription	Osteobl	bone
33	chr19:52852800-52857000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:52852800-52857000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:52853400-52857200	Weak transcription	HSMMtube	muscle
36	chr19:52853400-52858400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:52853600-52857000	Weak transcription	Primary B cells from cord blood	blood
38	chr19:52853600-52857000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:52853600-52858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:52854000-52857400	Weak transcription	Brain Substantia Nigra	brain
41	chr19:52854200-52857000	Weak transcription	Placenta	Placenta
42	chr19:52854200-52860400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:52854600-52861200	Strong transcription	Fetal Muscle Leg	muscle
44	chr19:52854800-52859400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
45	chr19:52855200-52857000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:52855200-52857000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:52855200-52857000	Weak transcription	Gastric	stomach
48	chr19:52855200-52859000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:52855200-52860600	Strong transcription	Fetal Stomach	stomach
50	chr19:52855400-52857000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links