Variant report

Variant	rs1646260
Chromosome Location	chr16:58768855-58768856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:58768851-58769308	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr16:58768726-58769347	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr16:58768725-58769508	HUVEC	blood vessel:	n/a	n/a
4	GATA2	chr16:58768791-58769355	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr16:58768781-58769403	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr16:58768842-58769376	HUVEC	blood vessel:	n/a	chr16:58769119-58769128

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:58768371..58769991-chr16:58770369..58773348,2	K562	blood:
2	chr16:58748643..58751250-chr16:58767584..58769117,2	K562	blood:

Variant related genes	Relation type
GOT2	TF binding region
ENSG00000125166	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1058192	0.83[AMR][1000 genomes]
rs11076259	0.88[EUR][1000 genomes]
rs11076260	0.88[EUR][1000 genomes]
rs12325516	0.87[EUR][1000 genomes]
rs12709012	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12924243	0.83[EUR][1000 genomes]
rs1369933	0.88[EUR][1000 genomes]
rs1369934	0.88[EUR][1000 genomes]
rs14221	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs149479	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs154435	0.86[EUR][1000 genomes]
rs1595180	0.88[EUR][1000 genomes]
rs1616072	0.90[EUR][1000 genomes]
rs1618602	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1624301	0.88[EUR][1000 genomes]
rs1626006	0.88[EUR][1000 genomes]
rs1646256	0.88[EUR][1000 genomes]
rs1646265	0.88[EUR][1000 genomes]
rs1646268	0.90[EUR][1000 genomes]
rs1646269	0.90[EUR][1000 genomes]
rs1646274	0.89[EUR][1000 genomes]
rs1646275	0.88[EUR][1000 genomes]
rs1646278	0.88[EUR][1000 genomes]
rs1646279	0.88[EUR][1000 genomes]
rs1646280	0.89[EUR][1000 genomes]
rs1646281	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646282	0.91[EUR][1000 genomes]
rs1646284	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1646285	0.88[EUR][1000 genomes]
rs1646286	0.88[EUR][1000 genomes]
rs1646287	0.88[EUR][1000 genomes]
rs1646288	0.88[EUR][1000 genomes]
rs1657161	0.90[EUR][1000 genomes]
rs1657163	0.91[EUR][1000 genomes]
rs1657164	0.89[EUR][1000 genomes]
rs1657166	0.82[EUR][1000 genomes]
rs1657167	0.89[EUR][1000 genomes]
rs1657169	0.85[EUR][1000 genomes]
rs1657171	0.84[EUR][1000 genomes]
rs1657176	0.96[EUR][1000 genomes]
rs1657177	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1657178	0.98[EUR][1000 genomes]
rs166290	0.81[EUR][1000 genomes]
rs171786	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs185397	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs187277	0.82[EUR][1000 genomes]
rs191783	0.88[EUR][1000 genomes]
rs2432621	0.87[EUR][1000 genomes]
rs2432622	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2575374	0.89[EUR][1000 genomes]
rs257616	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257617	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257619	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257621	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257624	0.88[EUR][1000 genomes]
rs257627	0.88[EUR][1000 genomes]
rs257628	0.88[EUR][1000 genomes]
rs257629	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs257631	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257632	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257633	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257637	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs257650	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs30834	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs30835	0.81[EUR][1000 genomes]
rs30836	0.87[EUR][1000 genomes]
rs30837	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs30838	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30839	0.83[EUR][1000 genomes]
rs30840	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs30841	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs30842	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40575	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4238801	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4315316	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4538000	0.90[EUR][1000 genomes]
rs4575523	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4784977	0.91[EUR][1000 genomes]
rs6993	0.82[EUR][1000 genomes]
rs7188608	0.96[EUR][1000 genomes]
rs727484	0.88[EUR][1000 genomes]
rs72792430	0.91[EUR][1000 genomes]
rs8044542	0.87[EUR][1000 genomes]
rs8045466	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8046154	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8049462	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8051078	0.88[EUR][1000 genomes]
rs8054414	0.87[EUR][1000 genomes]
rs8060717	0.88[EUR][1000 genomes]
rs8060721	0.88[EUR][1000 genomes]
rs839418	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9937713	0.88[EUR][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	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
4	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
rs1646260	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs1646260	GOT2	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58768200-58770000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:58768400-58770000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:58768400-58773200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:58768600-58769000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr16:58768600-58769000	Enhancers	Primary B cells from peripheral blood	blood
6	chr16:58768600-58769000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr16:58768600-58769000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr16:58768600-58769000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr16:58768600-58769000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr16:58768600-58769000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr16:58768600-58769000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr16:58768600-58769000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:58768600-58769000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr16:58768600-58769000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr16:58768600-58769000	Enhancers	Brain Angular Gyrus	brain
16	chr16:58768600-58769000	Enhancers	Brain Cingulate Gyrus	brain
17	chr16:58768600-58769000	Enhancers	Brain Hippocampus Middle	brain
18	chr16:58768600-58769000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr16:58768600-58769000	Enhancers	Brain Substantia Nigra	brain
20	chr16:58768600-58769000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr16:58768600-58769000	Enhancers	Fetal Heart	heart
22	chr16:58768600-58769000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr16:58768600-58769000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr16:58768600-58769000	Enhancers	Hela-S3	cervix
25	chr16:58768600-58769000	Flanking Active TSS	HepG2	liver
26	chr16:58768600-58769000	Enhancers	HUVEC	blood vessel
27	chr16:58768600-58769200	Enhancers	HMEC	breast
28	chr16:58768600-58769200	Enhancers	NHEK	skin
29	chr16:58768600-58769600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr16:58768600-58770000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr16:58768600-58770800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr16:58768600-58770800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr16:58768600-58773000	Weak transcription	Fetal Intestine Large	intestine
34	chr16:58768600-58773000	Weak transcription	Fetal Intestine Small	intestine
35	chr16:58768600-58781000	Weak transcription	Colonic Mucosa	Colon
36	chr16:58768800-58769000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr16:58768800-58769000	Active TSS	Brain Anterior Caudate	brain
38	chr16:58768800-58769400	Enhancers	Dnd41	blood
39	chr16:58768800-58771800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr16:58768800-58773000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr16:58768800-58773200	Weak transcription	Liver	Liver
42	chr16:58768800-58775400	Weak transcription	Rectal Mucosa Donor 31	rectum

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