Variant report

Variant	rs1657178
Chromosome Location	chr16:58769204-58769205
allele	G/T
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	CTCF	chr16:58769100-58769250	HMEC	breast:	n/a	n/a
7	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	chr16:58766806..58768382-chr16:58768885..58771530,2	K562	blood:

Variant related genes	Relation type
GOT2	TF binding region
ENSG00000125166	Chromatin interaction
ENSG00000245768	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11076259	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11076260	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11076262	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs11649636	0.87[AMR][1000 genomes]
rs11649637	0.87[AMR][1000 genomes]
rs12325516	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12709012	0.90[EUR][1000 genomes]
rs12924243	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1369933	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1369934	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs14221	0.83[EUR][1000 genomes]
rs1473205	0.81[ASN][1000 genomes]
rs1473206	0.81[ASN][1000 genomes]
rs149479	0.92[EUR][1000 genomes]
rs154435	0.87[EUR][1000 genomes]
rs1595180	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1595181	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs1616072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1616798	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1618602	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1624301	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1626006	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646256	0.89[EUR][1000 genomes]
rs1646260	0.98[EUR][1000 genomes]
rs1646265	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646268	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1646269	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1646274	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1646275	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646278	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646279	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646280	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646281	0.90[EUR][1000 genomes]
rs1646282	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646284	0.90[EUR][1000 genomes]
rs1646285	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646286	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646287	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646288	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657161	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1657163	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657164	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657166	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1657167	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1657169	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657171	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1657176	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657177	0.98[EUR][1000 genomes]
rs1657179	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs166290	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs171786	0.83[EUR][1000 genomes]
rs185397	0.81[ASW][hapmap];0.83[EUR][1000 genomes]
rs1865836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs187277	0.83[EUR][1000 genomes]
rs191783	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406087	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2432621	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2432622	0.87[EUR][1000 genomes]
rs2575374	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs257616	0.81[ASW][hapmap];0.83[EUR][1000 genomes]
rs257617	0.83[EUR][1000 genomes]
rs257619	0.83[EUR][1000 genomes]
rs257620	0.81[ASW][hapmap]
rs257621	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs257624	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257627	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257628	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257629	0.90[EUR][1000 genomes]
rs257631	0.83[EUR][1000 genomes]
rs257632	0.83[EUR][1000 genomes]
rs257633	0.83[EUR][1000 genomes]
rs257637	0.83[EUR][1000 genomes]
rs257650	0.87[EUR][1000 genomes]
rs30834	0.93[EUR][1000 genomes]
rs30835	0.83[EUR][1000 genomes]
rs30836	0.88[EUR][1000 genomes]
rs30837	0.93[EUR][1000 genomes]
rs30838	0.94[EUR][1000 genomes]
rs30839	0.85[EUR][1000 genomes]
rs30840	0.92[EUR][1000 genomes]
rs30841	0.92[EUR][1000 genomes]
rs30842	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs40575	0.88[EUR][1000 genomes]
rs4238801	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4315316	0.90[EUR][1000 genomes]
rs4499224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4538000	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4575523	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4784977	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499974	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs6499976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6993	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs7188608	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72792430	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8044542	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8045466	0.90[EUR][1000 genomes]
rs8046154	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs8049462	0.90[EUR][1000 genomes]
rs8051078	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8054414	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8060717	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8060721	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839418	0.92[EUR][1000 genomes]
rs9937713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1657178	GOT2	cis	parietal	SCAN
rs1657178	CETP	cis	parietal	SCAN
rs1657178	GOT2	cis	cerebellum	SCAN
rs1657178	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs1657178	GOT2	cis	Thyroid	GTEx

Chromatin state (count:20 , 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	chr16:58768600-58769600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:58768600-58770000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr16:58768600-58770800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr16:58768600-58770800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:58768600-58773000	Weak transcription	Fetal Intestine Large	intestine
9	chr16:58768600-58773000	Weak transcription	Fetal Intestine Small	intestine
10	chr16:58768600-58781000	Weak transcription	Colonic Mucosa	Colon
11	chr16:58768800-58769400	Enhancers	Dnd41	blood
12	chr16:58768800-58771800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr16:58768800-58773000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr16:58768800-58773200	Weak transcription	Liver	Liver
15	chr16:58768800-58775400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr16:58769000-58769400	Flanking Active TSS	HUVEC	blood vessel
17	chr16:58769000-58770400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:58769200-58769600	Weak transcription	HMEC	breast
19	chr16:58769200-58769600	Weak transcription	NHEK	skin
20	chr16:58769200-58773200	Weak transcription	HepG2	liver

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