Variant report

Variant	rs1789055
Chromosome Location	chr18:28640003-28640004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11081678	0.85[ASN][1000 genomes]
rs1125877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126214	0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1126215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1595356	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1658101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1789037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866104	0.85[ASN][1000 genomes]
rs2019624	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559974	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1789055	DSC3	Cis_1M	lymphoblastoid	RTeQTL
rs1789055	DSC2	Cis_1M	lymphoblastoid	RTeQTL
rs1789055	FAM59A	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28631200-28640400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:28634400-28641800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:28636400-28645000	Weak transcription	Fetal Intestine Large	intestine
4	chr18:28636600-28640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:28636600-28644800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr18:28636600-28645200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr18:28636800-28641800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr18:28637000-28643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr18:28637000-28645000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr18:28637000-28647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr18:28637200-28649000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr18:28637800-28641800	Weak transcription	Fetal Lung	lung
13	chr18:28638000-28647400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr18:28638200-28649000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:28638400-28645400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr18:28639000-28647400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr18:28639200-28647600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr18:28639200-28648600	Weak transcription	Pancreas	Pancrea
19	chr18:28639400-28646800	Weak transcription	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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