Variant report

Variant	rs30840
Chromosome Location	chr16:58744069-58744070
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	chr16:58741476..58744157-chr16:58748760..58750425,2	K562	blood:

Variant related genes	Relation type
ENSG00000125166	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1058192	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11076259	0.83[EUR][1000 genomes]
rs11076260	0.83[EUR][1000 genomes]
rs12325516	0.82[EUR][1000 genomes]
rs12709012	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1369933	0.83[EUR][1000 genomes]
rs1369934	0.83[EUR][1000 genomes]
rs14221	0.93[AMR][1000 genomes]
rs149479	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154435	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1595180	0.83[EUR][1000 genomes]
rs1616072	0.84[EUR][1000 genomes]
rs1618602	0.80[AMR][1000 genomes];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	0.87[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	0.80[AMR][1000 genomes];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	0.85[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	0.80[AMR][1000 genomes];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	0.94[AMR][1000 genomes]
rs257638	0.83[AMR][1000 genomes]
rs257650	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30834	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30836	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs30837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30838	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30839	0.81[EUR][1000 genomes]
rs30841	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30842	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40575	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238801	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4315316	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4538000	0.84[EUR][1000 genomes]
rs4575523	0.85[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	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8046154	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8049462	0.80[AMR][1000 genomes];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]
rs839418	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9937713	0.82[EUR][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
rs30840	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs30840	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	chr16:58739000-58745000	Weak transcription	Colonic Mucosa	Colon
7	chr16:58739000-58746200	Strong transcription	Fetal Muscle Leg	muscle
8	chr16:58739000-58757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr16:58739200-58744200	Strong transcription	HMEC	breast
10	chr16:58739200-58745200	Weak transcription	HSMMtube	muscle
11	chr16:58739200-58746400	Strong transcription	Brain Hippocampus Middle	brain
12	chr16:58739200-58750400	Strong transcription	Fetal Stomach	stomach
13	chr16:58739200-58758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr16:58739200-58758000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr16:58739200-58758400	Strong transcription	Primary T cells from cord blood	blood
16	chr16:58739200-58759000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:58739200-58759600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:58739400-58747800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr16:58739400-58752000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr16:58739400-58758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:58739600-58744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr16:58739600-58746400	Strong transcription	K562	blood
23	chr16:58739600-58748200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr16:58739600-58753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr16:58739600-58757600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:58739600-58757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr16:58739600-58758000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr16:58739600-58758200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr16:58739600-58758400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:58739800-58744200	Strong transcription	Brain Germinal Matrix	brain
31	chr16:58739800-58744200	Strong transcription	Esophagus	oesophagus
32	chr16:58739800-58744200	Strong transcription	Fetal Lung	lung
33	chr16:58739800-58744600	Strong transcription	Fetal Intestine Small	intestine
34	chr16:58739800-58747800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr16:58739800-58750400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr16:58739800-58753400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:58739800-58757800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr16:58739800-58757800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr16:58739800-58757800	Strong transcription	Thymus	Thymus
40	chr16:58739800-58759200	Strong transcription	Dnd41	blood
41	chr16:58739800-58759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr16:58740000-58744400	Strong transcription	Brain Angular Gyrus	brain
43	chr16:58740000-58753200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr16:58740000-58755200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr16:58740200-58751200	Strong transcription	Liver	Liver
46	chr16:58740200-58754200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr16:58740400-58744200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr16:58740400-58744200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr16:58740400-58744400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr16:58740400-58746200	Strong transcription	Primary neutrophils fromperipheralblood	blood

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