Variant report

Variant	rs1789045
Chromosome Location	chr18:28624397-28624398
allele	A/C
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	KAP1	chr18:28623901-28624564	HEK293	kidney:	n/a	chr18:28624190-28624198

Variant related genes	Relation type
DSC3	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1313593	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs1313594	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1313596	0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1313599	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1313693	0.82[JPT][hapmap]
rs1658096	0.82[GIH][hapmap]
rs166724	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs166725	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs169347	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs175777	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1789046	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790666	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202439	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs276911	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs276912	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs276913	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs276915	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs276916	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs276920	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs276922	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs276923	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs276932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276935	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs276940	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs276942	0.84[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs276943	0.85[GIH][hapmap]
rs276944	0.84[CEU][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	esv3388313	chr18:28583296-28693160	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv961134	chr18:28612225-28625943	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3369910	chr18:28624139-28624435	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1789045	DSC1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28623200-28625600	Weak transcription	Esophagus	oesophagus
2	chr18:28623200-28627600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:28623400-28624600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr18:28623400-28624800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr18:28623400-28627400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr18:28623400-28627600	Enhancers	NHEK	skin
7	chr18:28623400-28627800	Enhancers	HMEC	breast
8	chr18:28623400-28629800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr18:28624200-28624400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum

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