Variant report

Variant	rs1313693
Chromosome Location	chr18:28594909-28594910
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:28594378..28596048-chr18:28599359..28602223,2	MCF-7	breast:
2	chr18:28592790..28595531-chr18:28608278..28610485,2	MCF-7	breast:
3	chr18:28594117..28596433-chr18:28615710..28618191,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1110175	0.86[CEU][hapmap]
rs1313593	0.95[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1313594	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1313596	0.83[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1617054	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs166724	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs169347	0.95[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1789045	0.82[JPT][hapmap]
rs1790700	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs202439	0.95[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276911	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276912	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276913	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276914	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276915	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276916	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276917	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276920	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276922	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs276923	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs276932	0.82[JPT][hapmap]
rs276940	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276941	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276942	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276944	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs276945	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833613	chr18:28446454-28623599	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1313693	DSC2	Cis_1M	lymphoblastoid	RTeQTL
rs1313693	DSC3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28566200-28600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:28585800-28600600	Weak transcription	Esophagus	oesophagus
3	chr18:28588600-28595400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr18:28591600-28595800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr18:28592400-28595600	Weak transcription	NHEK	skin
6	chr18:28592600-28614800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:28593600-28611600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr18:28594000-28601200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr18:28594000-28611800	Strong transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links