Variant report

Variant	rs1657179
Chromosome Location	chr16:58769019-58769020
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
1	chr16:58768371..58769991-chr16:58770369..58773348,2	K562	blood:
2	chr16:58766806..58768382-chr16:58768885..58771530,2	K562	blood:
3	chr16:58748643..58751250-chr16:58767584..58769117,2	K562	blood:

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

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11076262	0.83[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs11076263	0.81[EUR][1000 genomes]
rs11646756	0.81[EUR][1000 genomes]
rs12325054	0.83[EUR][1000 genomes]
rs12325510	0.82[EUR][1000 genomes]
rs12595974	0.96[CEU][hapmap]
rs12598527	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs12600201	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12600206	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12935488	0.81[EUR][1000 genomes]
rs1364346	0.82[EUR][1000 genomes]
rs1424245	0.82[EUR][1000 genomes]
rs1473205	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473206	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151817	0.91[EUR][1000 genomes]
rs1595181	0.83[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs1615326	0.96[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs1616072	0.87[JPT][hapmap]
rs1616798	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627257	0.81[EUR][1000 genomes]
rs1628029	0.81[EUR][1000 genomes]
rs1646262	0.81[EUR][1000 genomes]
rs1646268	0.80[ASN][1000 genomes]
rs1646269	0.80[ASN][1000 genomes]
rs1646270	0.86[EUR][1000 genomes]
rs1646273	0.84[EUR][1000 genomes]
rs1646276	0.83[EUR][1000 genomes]
rs1646277	0.83[EUR][1000 genomes]
rs1646282	0.81[ASN][1000 genomes]
rs1646283	0.82[EUR][1000 genomes]
rs1646289	0.82[EUR][1000 genomes]
rs1646290	0.82[EUR][1000 genomes]
rs1657161	0.80[ASN][1000 genomes]
rs1657162	0.86[EUR][1000 genomes]
rs1657165	0.84[EUR][1000 genomes]
rs1657168	0.83[EUR][1000 genomes]
rs1657175	0.82[EUR][1000 genomes]
rs1657176	0.81[ASN][1000 genomes]
rs1657178	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs185397	0.91[CHD][hapmap]
rs1865836	0.87[JPT][hapmap]
rs244919	0.91[EUR][1000 genomes]
rs257616	0.91[CHD][hapmap]
rs257620	0.91[CHD][hapmap]
rs257621	0.81[JPT][hapmap]
rs257623	0.81[EUR][1000 genomes]
rs257625	0.81[EUR][1000 genomes]
rs257626	0.81[EUR][1000 genomes]
rs30843	0.89[EUR][1000 genomes]
rs4499224	0.86[JPT][hapmap]
rs4784977	0.82[ASN][1000 genomes]
rs62066815	0.82[EUR][1000 genomes]
rs62066843	0.81[EUR][1000 genomes]
rs6499974	0.84[JPT][hapmap]
rs6499976	0.87[JPT][hapmap]
rs7188608	0.81[ASN][1000 genomes]
rs727484	0.87[JPT][hapmap]
rs982848	0.91[EUR][1000 genomes]
rs9937713	0.85[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1657179	CETP	cis	parietal	SCAN
rs1657179	IRX5	cis	cerebellum	SCAN
rs1657179	GOT2	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr16:58768600-58769200	Enhancers	HMEC	breast
5	chr16:58768600-58769200	Enhancers	NHEK	skin
6	chr16:58768600-58769600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr16:58768600-58770000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr16:58768600-58770800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr16:58768600-58770800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:58768600-58773000	Weak transcription	Fetal Intestine Large	intestine
11	chr16:58768600-58773000	Weak transcription	Fetal Intestine Small	intestine
12	chr16:58768600-58781000	Weak transcription	Colonic Mucosa	Colon
13	chr16:58768800-58769400	Enhancers	Dnd41	blood
14	chr16:58768800-58771800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr16:58768800-58773000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:58768800-58773200	Weak transcription	Liver	Liver
17	chr16:58768800-58775400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr16:58769000-58769200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr16:58769000-58769200	Enhancers	HepG2	liver
20	chr16:58769000-58769400	Flanking Active TSS	HUVEC	blood vessel
21	chr16:58769000-58770400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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