Variant report

Variant	rs6993
Chromosome Location	chr16:58741367-58741368
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: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12600201	0.85[MEX][hapmap]
rs12600206	0.85[MEX][hapmap]
rs149479	0.82[EUR][1000 genomes]
rs151817	0.84[ASN][1000 genomes]
rs1615326	0.90[MEX][hapmap]
rs1616072	0.88[CEU][hapmap]
rs1618602	0.88[CEU][hapmap]
rs1646256	0.91[EUR][1000 genomes]
rs1646260	0.82[EUR][1000 genomes]
rs1646267	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1657176	0.83[EUR][1000 genomes]
rs1657177	0.82[EUR][1000 genomes]
rs1657178	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1865836	0.88[CEU][hapmap]
rs190473	0.90[AMR][1000 genomes]
rs244919	0.84[ASN][1000 genomes]
rs257618	0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs257634	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs257649	0.84[AMR][1000 genomes]
rs30834	0.81[EUR][1000 genomes]
rs30835	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30836	0.90[EUR][1000 genomes]
rs30837	0.81[EUR][1000 genomes]
rs30838	0.82[EUR][1000 genomes]
rs30839	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30840	0.82[EUR][1000 genomes]
rs30841	0.82[EUR][1000 genomes]
rs30842	0.88[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs30843	0.87[ASN][1000 genomes]
rs4238801	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs4499224	0.86[CEU][hapmap]
rs4575523	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs6499974	0.82[CEU][hapmap]
rs6499976	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap]
rs7188608	0.82[EUR][1000 genomes]
rs727484	0.88[CEU][hapmap]
rs8046154	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs839418	0.82[EUR][1000 genomes]
rs863944	0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs982848	0.84[ASN][1000 genomes]
rs9937713	0.87[CEU][hapmap]

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	nsv984340	chr16:58741302-58743315	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6993	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs6993	GOT2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58719200-58741800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:58735800-58752000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:58737400-58741800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:58737600-58742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:58737600-58743000	Weak transcription	HUVEC	blood vessel
6	chr16:58738200-58757800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:58738200-58758000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:58738400-58759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
10	chr16:58739000-58743600	Strong transcription	Fetal Thymus	thymus
11	chr16:58739000-58745000	Weak transcription	Colonic Mucosa	Colon
12	chr16:58739000-58746200	Strong transcription	Fetal Muscle Leg	muscle
13	chr16:58739000-58757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr16:58739200-58743400	Weak transcription	Fetal Kidney	kidney
15	chr16:58739200-58743800	Strong transcription	Brain Anterior Caudate	brain
16	chr16:58739200-58744200	Strong transcription	HMEC	breast
17	chr16:58739200-58745200	Weak transcription	HSMMtube	muscle
18	chr16:58739200-58746400	Strong transcription	Brain Hippocampus Middle	brain
19	chr16:58739200-58750400	Strong transcription	Fetal Stomach	stomach
20	chr16:58739200-58758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr16:58739200-58758000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr16:58739200-58758400	Strong transcription	Primary T cells from cord blood	blood
23	chr16:58739200-58759000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr16:58739200-58759600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr16:58739400-58743600	Strong transcription	Lung	lung
26	chr16:58739400-58747800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr16:58739400-58752000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr16:58739400-58758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr16:58739600-58742400	Strong transcription	Pancreas	Pancrea
30	chr16:58739600-58742600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:58739600-58743800	Strong transcription	NHEK	skin
32	chr16:58739600-58744000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr16:58739600-58744000	Strong transcription	Fetal Brain Female	brain
34	chr16:58739600-58744000	Strong transcription	A549	lung
35	chr16:58739600-58744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr16:58739600-58746400	Strong transcription	K562	blood
37	chr16:58739600-58748200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:58739600-58753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr16:58739600-58757600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr16:58739600-58757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:58739600-58758000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr16:58739600-58758200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr16:58739600-58758400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr16:58739800-58741400	Strong transcription	Fetal Heart	heart
45	chr16:58739800-58742400	Strong transcription	Hela-S3	cervix
46	chr16:58739800-58743600	Strong transcription	Spleen	Spleen
47	chr16:58739800-58743800	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr16:58739800-58743800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr16:58739800-58744000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr16:58739800-58744200	Strong transcription	Brain Germinal Matrix	brain

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