Variant report

Variant	rs190473
Chromosome Location	chr16:58754094-58754095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr16:58753912-58755672	HepG2	liver:	n/a	chr16:58754274-58754286

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:58751934..58754390-chr16:58755126..58757009,2	K562	blood:

Variant related genes	Relation type
GOT2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs14221	0.82[EUR][1000 genomes]
rs1646267	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646270	0.80[ASN][1000 genomes]
rs171786	0.82[EUR][1000 genomes]
rs173992	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs183757	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs185397	0.82[EUR][1000 genomes]
rs187277	0.82[EUR][1000 genomes]
rs257616	0.82[EUR][1000 genomes]
rs257617	0.82[EUR][1000 genomes]
rs257618	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257619	0.82[EUR][1000 genomes]
rs257621	0.82[EUR][1000 genomes]
rs257630	0.88[EUR][1000 genomes]
rs257631	0.82[EUR][1000 genomes]
rs257632	0.82[EUR][1000 genomes]
rs257633	0.82[EUR][1000 genomes]
rs257634	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257637	0.82[EUR][1000 genomes]
rs30835	0.91[AMR][1000 genomes]
rs30839	0.90[AMR][1000 genomes]
rs30843	0.81[AMR][1000 genomes]
rs6993	0.90[AMR][1000 genomes]
rs863944	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs190473	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs190473	GOT2	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58738200-58757800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr16:58738200-58758000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:58738400-58759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
5	chr16:58739000-58757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:58739200-58758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:58739200-58758000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr16:58739200-58758400	Strong transcription	Primary T cells from cord blood	blood
9	chr16:58739200-58759000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:58739200-58759600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:58739400-58758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:58739600-58757600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:58739600-58757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:58739600-58758000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr16:58739600-58758200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr16:58739600-58758400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:58739800-58757800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr16:58739800-58757800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr16:58739800-58757800	Strong transcription	Thymus	Thymus
20	chr16:58739800-58759200	Strong transcription	Dnd41	blood
21	chr16:58739800-58759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr16:58740000-58755200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr16:58740200-58754200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:58740400-58756400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr16:58740400-58757800	Strong transcription	Fetal Intestine Large	intestine
26	chr16:58740400-58757800	Strong transcription	Ovary	ovary
27	chr16:58740400-58757800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr16:58740400-58758000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr16:58740400-58759000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr16:58740600-58757800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr16:58743000-58757800	Strong transcription	HUVEC	blood vessel
32	chr16:58743400-58759000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:58744800-58757800	Strong transcription	Fetal Brain Female	brain
34	chr16:58745000-58757800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr16:58745000-58757800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr16:58745000-58757800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr16:58745000-58758400	Strong transcription	Left Ventricle	heart
38	chr16:58745200-58757600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr16:58745200-58758400	Strong transcription	Osteobl	bone
40	chr16:58745400-58758000	Strong transcription	Fetal Intestine Small	intestine
41	chr16:58745600-58757800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:58747200-58757600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr16:58747600-58757800	Strong transcription	Fetal Muscle Leg	muscle
44	chr16:58747800-58767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr16:58748000-58756600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr16:58748000-58757200	Strong transcription	Brain Germinal Matrix	brain
47	chr16:58748800-58755800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr16:58748800-58757200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:58748800-58757600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr16:58748800-58757600	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links