Variant report

Variant	rs2004290
Chromosome Location	chr4:106347401-106347402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1077526	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.83[EUR][1000 genomes]
rs17035550	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035553	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035581	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035584	1.00[ASN][1000 genomes]
rs17035586	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035619	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509136	1.00[ASN][1000 genomes]
rs3898404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499701	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652556	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56397029	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59902936	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs6533194	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517713	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66763438	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932244	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67248885	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67476913	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829168	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.84[EUR][1000 genomes]
rs72668208	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668215	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2004290	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:106309400-106351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
5	chr4:106321600-106356200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:106321800-106353600	Weak transcription	HMEC	breast
7	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
8	chr4:106326000-106356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:106326000-106356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:106326000-106363200	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:106326200-106347600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:106327200-106365200	Weak transcription	Osteobl	bone
13	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
14	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:106330600-106356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:106334800-106347600	Weak transcription	A549	lung
17	chr4:106336400-106347600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:106336400-106347600	Weak transcription	NHEK	skin
19	chr4:106336600-106356400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:106336800-106347600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:106336800-106376400	Weak transcription	Right Ventricle	heart
22	chr4:106336800-106387800	Weak transcription	NHLF	lung
23	chr4:106337000-106354400	Weak transcription	Left Ventricle	heart
24	chr4:106337000-106354600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:106337200-106356600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:106338000-106347600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:106340200-106347600	Weak transcription	Brain Angular Gyrus	brain
28	chr4:106340200-106387800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:106341600-106347600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:106341600-106376000	Weak transcription	Fetal Heart	heart
31	chr4:106342800-106348200	Strong transcription	Liver	Liver
32	chr4:106342800-106348600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:106343200-106363000	Weak transcription	Psoas Muscle	Psoas
34	chr4:106343600-106349000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:106344000-106363800	Weak transcription	HepG2	liver
36	chr4:106344200-106352800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:106344400-106348200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:106344400-106349400	Strong transcription	Primary T cells from cord blood	blood
39	chr4:106344800-106347600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:106344800-106347600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:106345200-106350800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:106345200-106354400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:106345200-106354800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:106345200-106358800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:106345800-106347600	Strong transcription	K562	blood
46	chr4:106345800-106347800	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr4:106346000-106347800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
48	chr4:106346000-106350600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:106346200-106347600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:106346200-106348200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links