Variant report

Variant	rs7236469
Chromosome Location	chr18:29076004-29076005
allele	C/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	chr18:29075733-29076558	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DSG2	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1350731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1460602	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs17660585	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1824477	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1841396	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2212617	0.89[ASN][1000 genomes]
rs2212618	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2219584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704050	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704051	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704052	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704053	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704055	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2848677	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848680	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848681	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4799310	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4799573	1.00[ASN][1000 genomes]
rs6506927	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6506928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7227343	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7227984	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231288	0.98[ASN][1000 genomes]
rs7231553	0.98[ASN][1000 genomes]
rs7232282	1.00[ASN][1000 genomes]
rs7235272	0.98[ASN][1000 genomes]
rs7236324	1.00[ASN][1000 genomes]
rs7238729	0.98[ASN][1000 genomes]
rs7239805	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7240824	0.83[ASN][1000 genomes]
rs7240920	0.90[ASN][1000 genomes]
rs7241107	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73414280	0.99[ASN][1000 genomes]
rs73953901	1.00[ASN][1000 genomes]
rs9304097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9304098	0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9304099	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9941421	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9945031	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9945420	0.88[ASN][1000 genomes]
rs9951843	0.94[ASN][1000 genomes]
rs9961910	0.96[ASN][1000 genomes]
rs9961920	1.00[ASN][1000 genomes]
rs9961925	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962121	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9962318	1.00[ASN][1000 genomes]
rs9962333	0.88[ASN][1000 genomes]
rs9962423	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7236469	DSC1	cis	parietal	SCAN
rs7236469	RP11-650P15.1	cis	Thyroid	GTEx
rs7236469	TAF4B	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29067600-29076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:29071200-29077200	Weak transcription	Fetal Intestine Small	intestine
3	chr18:29071800-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr18:29071800-29077400	Weak transcription	HMEC	breast
5	chr18:29072000-29077200	Weak transcription	NHEK	skin
6	chr18:29072000-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:29072200-29077600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr18:29074200-29077200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr18:29074400-29077400	Weak transcription	GM12878-XiMat	blood
10	chr18:29074800-29077400	Weak transcription	Colonic Mucosa	Colon
11	chr18:29075200-29077200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links