Variant report

Variant	rs839418
Chromosome Location	chr16:58739330-58739331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1058192	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11076259	0.83[EUR][1000 genomes]
rs11076260	0.83[EUR][1000 genomes]
rs12325516	0.82[EUR][1000 genomes]
rs12709012	0.83[EUR][1000 genomes]
rs1369933	0.83[EUR][1000 genomes]
rs1369934	0.83[EUR][1000 genomes]
rs14221	0.90[AMR][1000 genomes]
rs149479	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154435	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1595180	0.83[EUR][1000 genomes]
rs1616072	0.84[EUR][1000 genomes]
rs1618602	0.83[EUR][1000 genomes]
rs1624301	0.83[EUR][1000 genomes]
rs1626006	0.83[EUR][1000 genomes]
rs1646256	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1646260	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1646265	0.83[EUR][1000 genomes]
rs1646268	0.84[EUR][1000 genomes]
rs1646269	0.84[EUR][1000 genomes]
rs1646274	0.84[EUR][1000 genomes]
rs1646275	0.83[EUR][1000 genomes]
rs1646278	0.83[EUR][1000 genomes]
rs1646279	0.83[EUR][1000 genomes]
rs1646280	0.82[EUR][1000 genomes]
rs1646281	0.83[EUR][1000 genomes]
rs1646282	0.85[EUR][1000 genomes]
rs1646284	0.83[EUR][1000 genomes]
rs1646285	0.82[EUR][1000 genomes]
rs1646286	0.83[EUR][1000 genomes]
rs1646287	0.83[EUR][1000 genomes]
rs1646288	0.83[EUR][1000 genomes]
rs1657161	0.84[EUR][1000 genomes]
rs1657163	0.85[EUR][1000 genomes]
rs1657164	0.84[EUR][1000 genomes]
rs1657167	0.83[EUR][1000 genomes]
rs1657176	0.91[EUR][1000 genomes]
rs1657177	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1657178	0.92[EUR][1000 genomes]
rs171786	0.91[AMR][1000 genomes]
rs185397	0.91[AMR][1000 genomes]
rs187277	0.89[AMR][1000 genomes]
rs191783	0.83[EUR][1000 genomes]
rs2432621	0.81[EUR][1000 genomes]
rs2432622	0.80[EUR][1000 genomes]
rs2575374	0.83[EUR][1000 genomes]
rs257616	0.91[AMR][1000 genomes]
rs257617	0.91[AMR][1000 genomes]
rs257619	0.91[AMR][1000 genomes]
rs257621	0.91[AMR][1000 genomes]
rs257624	0.83[EUR][1000 genomes]
rs257627	0.83[EUR][1000 genomes]
rs257628	0.83[EUR][1000 genomes]
rs257629	0.83[EUR][1000 genomes]
rs257631	0.91[AMR][1000 genomes]
rs257632	0.91[AMR][1000 genomes]
rs257633	0.91[AMR][1000 genomes]
rs257636	0.87[AMR][1000 genomes]
rs257637	0.91[AMR][1000 genomes]
rs257638	0.83[AMR][1000 genomes]
rs257650	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30834	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30836	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs30837	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30838	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30839	0.81[EUR][1000 genomes]
rs30840	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30841	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30842	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40575	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4238801	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4315316	0.83[EUR][1000 genomes]
rs4538000	0.84[EUR][1000 genomes]
rs4575523	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4784977	0.85[EUR][1000 genomes]
rs6993	0.82[EUR][1000 genomes]
rs7188608	0.90[EUR][1000 genomes]
rs727484	0.83[EUR][1000 genomes]
rs72792430	0.85[EUR][1000 genomes]
rs8044542	0.82[EUR][1000 genomes]
rs8045466	0.83[EUR][1000 genomes]
rs8046154	0.82[EUR][1000 genomes]
rs8049462	0.83[EUR][1000 genomes]
rs8051078	0.82[EUR][1000 genomes]
rs8054414	0.82[EUR][1000 genomes]
rs8060717	0.83[EUR][1000 genomes]
rs8060721	0.83[EUR][1000 genomes]
rs9937713	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv510686	chr16:58646119-58765894	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs839418	GOT2	cis	Thyroid	GTEx
rs839418	GOT2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58719000-58739600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr16:58719200-58741800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr16:58731000-58740000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:58731200-58739600	Weak transcription	Fetal Brain Female	brain
5	chr16:58732000-58739600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:58732000-58739600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr16:58732200-58739400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr16:58732400-58740600	Weak transcription	Fetal Brain Male	brain
9	chr16:58733200-58739600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:58733200-58739600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr16:58733200-58740600	Weak transcription	GM12878-XiMat	blood
12	chr16:58733200-58740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:58733400-58740400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr16:58733400-58740600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr16:58733400-58741000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr16:58733600-58740400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr16:58733800-58740400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr16:58734200-58740600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr16:58735600-58739600	Weak transcription	A549	lung
20	chr16:58735600-58739800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr16:58735600-58739800	Weak transcription	Thymus	Thymus
22	chr16:58735800-58752000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr16:58736000-58740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr16:58736200-58739400	Weak transcription	Left Ventricle	heart
25	chr16:58736200-58739800	Weak transcription	Brain Germinal Matrix	brain
26	chr16:58736200-58740400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr16:58736200-58740400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr16:58736200-58741200	Weak transcription	Osteobl	bone
29	chr16:58736400-58739800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr16:58736400-58739800	Weak transcription	Fetal Intestine Small	intestine
31	chr16:58736800-58740800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:58737200-58739800	Weak transcription	Fetal Lung	lung
33	chr16:58737400-58741800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:58737600-58739600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:58737600-58739800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr16:58737600-58739800	Weak transcription	Esophagus	oesophagus
37	chr16:58737600-58742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:58737600-58743000	Weak transcription	HUVEC	blood vessel
39	chr16:58737800-58739400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:58737800-58739400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr16:58737800-58739400	Weak transcription	Lung	lung
42	chr16:58737800-58739600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr16:58737800-58739600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr16:58737800-58739600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr16:58737800-58739600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr16:58738000-58739600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr16:58738000-58739600	Weak transcription	K562	blood
48	chr16:58738000-58739600	Weak transcription	NHEK	skin
49	chr16:58738000-58739800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr16:58738000-58739800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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