Variant report

Variant	rs173992
Chromosome Location	chr16:58760478-58760479
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1058192	0.87[EUR][1000 genomes]
rs12325054	0.81[ASN][1000 genomes]
rs12325510	0.81[ASN][1000 genomes]
rs1364346	0.81[ASN][1000 genomes]
rs14221	0.91[EUR][1000 genomes]
rs1615326	0.81[ASN][1000 genomes]
rs1627257	0.81[ASN][1000 genomes]
rs1628029	0.81[ASN][1000 genomes]
rs1646262	0.81[ASN][1000 genomes]
rs1646267	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646270	0.84[ASN][1000 genomes]
rs1646276	0.81[ASN][1000 genomes]
rs1646277	0.81[ASN][1000 genomes]
rs1646283	0.81[ASN][1000 genomes]
rs1646289	0.81[ASN][1000 genomes]
rs1646290	0.81[ASN][1000 genomes]
rs1657162	0.82[ASN][1000 genomes]
rs1657165	0.81[ASN][1000 genomes]
rs1657175	0.81[ASN][1000 genomes]
rs171786	0.91[EUR][1000 genomes]
rs183757	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs185397	0.91[EUR][1000 genomes]
rs187277	0.91[EUR][1000 genomes]
rs190473	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs257616	0.91[EUR][1000 genomes]
rs257617	0.91[EUR][1000 genomes]
rs257618	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257619	0.91[EUR][1000 genomes]
rs257621	0.91[EUR][1000 genomes]
rs257623	0.81[ASN][1000 genomes]
rs257626	0.81[ASN][1000 genomes]
rs257630	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs257631	0.91[EUR][1000 genomes]
rs257632	0.91[EUR][1000 genomes]
rs257633	0.91[EUR][1000 genomes]
rs257634	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257636	0.86[EUR][1000 genomes]
rs257637	0.91[EUR][1000 genomes]
rs257638	0.88[EUR][1000 genomes]
rs62066815	0.81[ASN][1000 genomes]
rs62066843	0.81[ASN][1000 genomes]
rs863944	0.90[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
rs173992	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs173992	GOT2	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
2	chr16:58747800-58767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:58752600-58766600	Weak transcription	NHLF	lung
4	chr16:58753000-58766000	Weak transcription	Small Intestine	intestine
5	chr16:58753200-58765600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:58753200-58766400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:58753200-58766600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:58753200-58766800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:58753400-58766400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr16:58754000-58761000	Weak transcription	Pancreas	Pancrea
11	chr16:58754000-58766800	Weak transcription	Esophagus	oesophagus
12	chr16:58755200-58766800	Weak transcription	Fetal Lung	lung
13	chr16:58755400-58761400	Weak transcription	Psoas Muscle	Psoas
14	chr16:58755400-58766800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:58755600-58761400	Weak transcription	Fetal Heart	heart
16	chr16:58755600-58764200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr16:58755600-58766400	Weak transcription	Fetal Brain Male	brain
18	chr16:58756200-58761000	Weak transcription	Right Ventricle	heart
19	chr16:58756200-58764200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr16:58756200-58766800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:58756200-58766800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr16:58756200-58766800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr16:58756400-58761600	Weak transcription	Spleen	Spleen
24	chr16:58756400-58766400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr16:58757000-58766200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:58757000-58766600	Weak transcription	Colonic Mucosa	Colon
27	chr16:58757000-58767400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:58757200-58761600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr16:58757200-58766600	Weak transcription	Brain Germinal Matrix	brain
30	chr16:58757400-58761400	Weak transcription	Fetal Kidney	kidney
31	chr16:58757400-58765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr16:58757400-58766200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr16:58757600-58761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr16:58757600-58761600	Weak transcription	GM12878-XiMat	blood
35	chr16:58757600-58763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr16:58757600-58764000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr16:58757600-58765600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr16:58757600-58766200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:58757600-58766200	Weak transcription	A549	lung
40	chr16:58757600-58766200	Weak transcription	NH-A	brain
41	chr16:58757600-58766600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr16:58757600-58766600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr16:58757600-58767000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr16:58757800-58761000	Enhancers	Liver	Liver
45	chr16:58757800-58761000	Weak transcription	Brain Substantia Nigra	brain
46	chr16:58757800-58761000	Weak transcription	Gastric	stomach
47	chr16:58757800-58761400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr16:58757800-58761400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr16:58757800-58761400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr16:58757800-58761400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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