Variant report

Variant	rs4325646
Chromosome Location	chr18:28744391-28744392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1370450	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437605	0.88[EUR][1000 genomes]
rs1437608	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1437609	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1816632	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1816633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118341	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2118342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164765	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254170	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2254172	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577073	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2741000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2741004	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851996	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344831	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4361001	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6506886	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506891	0.89[JPT][hapmap]
rs6506892	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7238415	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7243239	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs8090853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951298	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs976749	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976750	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976751	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs991482	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9947328	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9948366	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9952351	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9955032	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9955430	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9960487	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	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
2	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv132191	chr18:28739028-28745912	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv131242	chr18:28739028-28748058	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4325646	DSC1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28737400-28746400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr18:28742800-28746600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:28743200-28744600	Enhancers	Primary T cells from cord blood	blood
4	chr18:28743200-28756000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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