Variant report

Variant	rs40575
Chromosome Location	chr16:58746906-58746907
allele	C/T
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: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1058192	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12709012	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs14221	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs149479	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154435	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1616072	0.81[EUR][1000 genomes]
rs1618602	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1646256	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1646260	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1646268	0.81[EUR][1000 genomes]
rs1646269	0.81[EUR][1000 genomes]
rs1646274	0.81[EUR][1000 genomes]
rs1646281	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1646282	0.82[EUR][1000 genomes]
rs1646284	0.80[AMR][1000 genomes]
rs1657161	0.81[EUR][1000 genomes]
rs1657163	0.82[EUR][1000 genomes]
rs1657164	0.81[EUR][1000 genomes]
rs1657167	0.80[EUR][1000 genomes]
rs1657176	0.87[EUR][1000 genomes]
rs1657177	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1657178	0.88[EUR][1000 genomes]
rs171786	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs185397	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs187277	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2432622	0.81[ASN][1000 genomes]
rs2575374	0.80[EUR][1000 genomes]
rs257616	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257617	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257619	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257621	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257629	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs257631	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257632	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257633	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257636	0.87[AMR][1000 genomes]
rs257637	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257638	0.83[AMR][1000 genomes]
rs257650	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs30834	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30836	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs30837	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30838	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30840	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs30841	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30842	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4238801	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4315316	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4538000	0.81[EUR][1000 genomes]
rs4575523	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4784977	0.82[EUR][1000 genomes]
rs7188608	0.87[EUR][1000 genomes]
rs72792430	0.82[EUR][1000 genomes]
rs8045466	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8046154	0.80[AMR][1000 genomes]
rs8049462	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs839418	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[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
rs40575	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs40575	GOT2	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58735800-58752000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:58738200-58757800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr16:58738200-58758000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:58738400-58759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
6	chr16:58739000-58757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:58739200-58750400	Strong transcription	Fetal Stomach	stomach
8	chr16:58739200-58758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr16:58739200-58758000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr16:58739200-58758400	Strong transcription	Primary T cells from cord blood	blood
11	chr16:58739200-58759000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:58739200-58759600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:58739400-58747800	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr16:58739400-58752000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr16:58739400-58758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr16:58739600-58748200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:58739600-58753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr16:58739600-58757600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr16:58739600-58757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr16:58739600-58758000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr16:58739600-58758200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr16:58739600-58758400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr16:58739800-58747800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:58739800-58750400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr16:58739800-58753400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr16:58739800-58757800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr16:58739800-58757800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr16:58739800-58757800	Strong transcription	Thymus	Thymus
29	chr16:58739800-58759200	Strong transcription	Dnd41	blood
30	chr16:58739800-58759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:58740000-58753200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:58740000-58755200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr16:58740200-58751200	Strong transcription	Liver	Liver
34	chr16:58740200-58754200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr16:58740400-58756400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr16:58740400-58757800	Strong transcription	Fetal Intestine Large	intestine
37	chr16:58740400-58757800	Strong transcription	Ovary	ovary
38	chr16:58740400-58757800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr16:58740400-58758000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr16:58740400-58759000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:58740600-58748000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr16:58740600-58752000	Weak transcription	Small Intestine	intestine
43	chr16:58740600-58757800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:58740800-58750400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:58741200-58748600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr16:58741200-58749600	Weak transcription	Aorta	Aorta
47	chr16:58741200-58750600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr16:58741400-58749000	Weak transcription	Fetal Heart	heart
49	chr16:58742000-58749800	Weak transcription	Fetal Brain Male	brain
50	chr16:58742200-58749200	Weak transcription	Primary B cells from peripheral blood	blood

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