Variant report

Variant	rs257650
Chromosome Location	chr16:58740341-58740342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:58739390..58742462-chr16:58745001..58747793,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1058192	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs14221	0.87[AMR][1000 genomes]
rs149479	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs154435	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1646256	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1646260	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1646282	0.80[EUR][1000 genomes]
rs1657163	0.80[EUR][1000 genomes]
rs1657176	0.86[EUR][1000 genomes]
rs1657177	0.86[EUR][1000 genomes]
rs1657178	0.87[EUR][1000 genomes]
rs171786	0.89[AMR][1000 genomes]
rs185397	0.89[AMR][1000 genomes]
rs187277	0.86[AMR][1000 genomes]
rs257616	0.89[AMR][1000 genomes]
rs257617	0.89[AMR][1000 genomes]
rs257619	0.89[AMR][1000 genomes]
rs257621	0.89[AMR][1000 genomes]
rs257631	0.89[AMR][1000 genomes]
rs257632	0.89[AMR][1000 genomes]
rs257633	0.89[AMR][1000 genomes]
rs257636	0.85[AMR][1000 genomes]
rs257637	0.88[AMR][1000 genomes]
rs257638	0.80[AMR][1000 genomes]
rs30834	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30836	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs30837	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30838	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs30840	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30841	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30842	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40575	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4238801	0.81[EUR][1000 genomes]
rs4575523	0.81[EUR][1000 genomes]
rs4784977	0.80[EUR][1000 genomes]
rs7188608	0.85[EUR][1000 genomes]
rs72792430	0.80[EUR][1000 genomes]
rs839418	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][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
rs257650	GOT2	cis	Thyroid	GTEx
rs257650	GOT2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58719200-58741800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:58732400-58740600	Weak transcription	Fetal Brain Male	brain
3	chr16:58733200-58740600	Weak transcription	GM12878-XiMat	blood
4	chr16:58733200-58740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr16:58733400-58740400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr16:58733400-58740600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:58733400-58741000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr16:58733600-58740400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr16:58733800-58740400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr16:58734200-58740600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr16:58735800-58752000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:58736000-58740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:58736200-58740400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr16:58736200-58740400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr16:58736200-58741200	Weak transcription	Osteobl	bone
16	chr16:58736800-58740800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr16:58737400-58741800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr16:58737600-58742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr16:58737600-58743000	Weak transcription	HUVEC	blood vessel
20	chr16:58738000-58740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:58738200-58740400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr16:58738200-58740400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:58738200-58740400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr16:58738200-58740400	Weak transcription	Adipose Nuclei	Adipose
25	chr16:58738200-58740400	Weak transcription	Brain Substantia Nigra	brain
26	chr16:58738200-58740400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr16:58738200-58757800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:58738200-58758000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:58738400-58740400	Weak transcription	Ovary	ovary
30	chr16:58738400-58740400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr16:58738400-58740800	Weak transcription	Primary B cells from cord blood	blood
32	chr16:58738400-58759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
34	chr16:58738600-58740400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr16:58738600-58740400	Weak transcription	Fetal Intestine Large	intestine
36	chr16:58738600-58740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:58738600-58741000	Weak transcription	Gastric	stomach
38	chr16:58738800-58740400	Weak transcription	NH-A	brain
39	chr16:58738800-58740600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr16:58738800-58740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr16:58738800-58740600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr16:58738800-58740600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr16:58738800-58740600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr16:58738800-58740600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr16:58738800-58740600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr16:58738800-58740600	Weak transcription	Colon Smooth Muscle	Colon
47	chr16:58738800-58740600	Weak transcription	Placenta	Placenta
48	chr16:58738800-58740600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr16:58738800-58741000	Weak transcription	NHLF	lung
50	chr16:58739000-58740800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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