Variant report

Variant	rs1623381
Chromosome Location	chr18:28640603-28640604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:28635410..28637896-chr18:28640436..28642394,2	K562	blood:
2	chr18:28635379..28636910-chr18:28640103..28642394,2	K562	blood:
3	chr18:28638090..28639722-chr18:28640416..28641974,2	K562	blood:
4	chr18:28640333..28642657-chr18:28648234..28652025,3	K562	blood:

Variant related genes	Relation type
ENSG00000261521	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1125876	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1658096	0.82[YRI][hapmap]
rs1658099	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1658100	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1658102	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790696	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276919	1.00[JPT][hapmap]
rs276943	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv2244	chr18:28635554-28666380	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1623381	DSG4	cis	parietal	SCAN
rs1623381	DSC2	cis	cerebellum	SCAN
rs1623381	DSC1	cis	parietal	SCAN
rs1623381	FAM59A	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28634400-28641800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:28636400-28645000	Weak transcription	Fetal Intestine Large	intestine
3	chr18:28636600-28644800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr18:28636600-28645200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr18:28636800-28641800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr18:28637000-28643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:28637000-28645000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr18:28637000-28647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr18:28637200-28649000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:28637800-28641800	Weak transcription	Fetal Lung	lung
11	chr18:28638000-28647400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr18:28638200-28649000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:28638400-28645400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr18:28639000-28647400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr18:28639200-28647600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr18:28639200-28648600	Weak transcription	Pancreas	Pancrea
17	chr18:28639400-28646800	Weak transcription	HepG2	liver
18	chr18:28640600-28641000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr18:28640600-28642400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr18:28640600-28648000	Weak transcription	Left Ventricle	heart
21	chr18:28640600-28648800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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