Variant report

Variant	rs1657176
Chromosome Location	chr16:58770737-58770738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:58768371..58769991-chr16:58770369..58773348,2	K562	blood:
2	chr16:58766806..58768382-chr16:58768885..58771530,2	K562	blood:
3	chr16:58769989..58772148-chr16:58777618..58779296,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245768	Chromatin interaction
ENSG00000125166	Chromatin interaction
ENSG00000200424	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11076259	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11076260	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11649636	0.89[AMR][1000 genomes]
rs11649637	0.89[AMR][1000 genomes]
rs12325516	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12709012	0.91[EUR][1000 genomes]
rs12924243	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1369933	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1369934	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs14221	0.82[EUR][1000 genomes]
rs1473205	0.81[ASN][1000 genomes]
rs1473206	0.81[ASN][1000 genomes]
rs149479	0.91[EUR][1000 genomes]
rs154435	0.86[EUR][1000 genomes]
rs1595180	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1616072	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1616798	0.81[ASN][1000 genomes]
rs1618602	0.91[EUR][1000 genomes]
rs1624301	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1626006	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646256	0.88[EUR][1000 genomes]
rs1646260	0.96[EUR][1000 genomes]
rs1646265	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1646269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1646274	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1646275	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646278	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646279	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646280	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646281	0.91[EUR][1000 genomes]
rs1646282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646284	0.91[EUR][1000 genomes]
rs1646285	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1646286	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646287	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646288	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657161	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1657163	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657164	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657166	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1657167	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1657169	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657171	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1657177	0.99[EUR][1000 genomes]
rs1657178	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657179	0.81[ASN][1000 genomes]
rs166290	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs171786	0.82[EUR][1000 genomes]
rs185397	0.82[EUR][1000 genomes]
rs187277	0.82[EUR][1000 genomes]
rs191783	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406087	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2432621	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2432622	0.88[EUR][1000 genomes]
rs2575374	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs257616	0.82[EUR][1000 genomes]
rs257617	0.82[EUR][1000 genomes]
rs257619	0.82[EUR][1000 genomes]
rs257621	0.82[EUR][1000 genomes]
rs257624	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257627	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257628	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257629	0.91[EUR][1000 genomes]
rs257631	0.82[EUR][1000 genomes]
rs257632	0.82[EUR][1000 genomes]
rs257633	0.82[EUR][1000 genomes]
rs257637	0.82[EUR][1000 genomes]
rs257650	0.86[EUR][1000 genomes]
rs30834	0.92[EUR][1000 genomes]
rs30835	0.82[EUR][1000 genomes]
rs30836	0.86[EUR][1000 genomes]
rs30837	0.92[EUR][1000 genomes]
rs30838	0.93[EUR][1000 genomes]
rs30839	0.84[EUR][1000 genomes]
rs30840	0.91[EUR][1000 genomes]
rs30841	0.91[EUR][1000 genomes]
rs30842	0.91[EUR][1000 genomes]
rs40575	0.87[EUR][1000 genomes]
rs4238801	0.94[EUR][1000 genomes]
rs4315316	0.91[EUR][1000 genomes]
rs4538000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4575523	0.94[EUR][1000 genomes]
rs4784977	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6993	0.83[EUR][1000 genomes]
rs7184377	0.81[EUR][1000 genomes]
rs7188608	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727484	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72792430	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8044542	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8045466	0.91[EUR][1000 genomes]
rs8046154	0.90[EUR][1000 genomes]
rs8049462	0.91[EUR][1000 genomes]
rs8051078	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8054414	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8060717	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8060721	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839418	0.91[EUR][1000 genomes]
rs899375	0.80[EUR][1000 genomes]
rs9937713	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1657176	GOT2	cis	Thyroid	GTEx
rs1657176	GOT2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58768400-58773200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:58768600-58770800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr16:58768600-58770800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:58768600-58773000	Weak transcription	Fetal Intestine Large	intestine
5	chr16:58768600-58773000	Weak transcription	Fetal Intestine Small	intestine
6	chr16:58768600-58781000	Weak transcription	Colonic Mucosa	Colon
7	chr16:58768800-58771800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr16:58768800-58773000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr16:58768800-58773200	Weak transcription	Liver	Liver
10	chr16:58768800-58775400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr16:58769200-58773200	Weak transcription	HepG2	liver
12	chr16:58769600-58770800	Enhancers	HMEC	breast
13	chr16:58770000-58770800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr16:58770400-58770800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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