Variant report

Variant	rs1790694
Chromosome Location	chr18:28642129-28642130
allele	C/T
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	RELA	chr18:28641859-28642717	GM12891	blood:	n/a	n/a
2	POLR2A	chr18:28641735-28642272	GM12891	blood:	n/a	n/a
3	POU2F2	chr18:28641867-28642264	GM12891	blood:	n/a	n/a
4	NFATC1	chr18:28641822-28642384	GM12878	blood:	n/a	n/a
5	MEF2A	chr18:28641911-28642355	GM12878	blood:	n/a	chr18:28642249-28642264 chr18:28642249-28642265 chr18:28642250-28642265 chr18:28642251-28642266 chr18:28642252-28642263 chr18:28642250-28642266 chr18:28642253-28642264 chr18:28642249-28642266
6	FOXM1	chr18:28641835-28642546	GM12878	blood:	n/a	n/a
7	EBF1	chr18:28641932-28642416	GM12878	blood:	n/a	n/a
8	NFIC	chr18:28641888-28642523	GM12878	blood:	n/a	n/a
9	CUX1	chr18:28642079-28642334	GM12878	blood:	n/a	n/a
10	RUNX3	chr18:28641928-28642476	GM12878	blood:	n/a	chr18:28642203-28642212 chr18:28642203-28642212
11	ATF2	chr18:28641878-28642432	GM12878	blood:	n/a	n/a
12	ATF2	chr18:28641762-28642485	GM12878	blood:	n/a	n/a
13	POLR2A	chr18:28641793-28642200	GM12891	blood:	n/a	n/a
14	STAT3	chr18:28642031-28642186	GM12878	blood:	n/a	n/a
15	RUNX3	chr18:28641797-28642576	GM12878	blood:	n/a	chr18:28642203-28642212 chr18:28642203-28642212
16	BCL3	chr18:28641839-28642386	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:28641189..28643310-chr18:28664453..28667293,2	K562	blood:
2	chr18:28635410..28637896-chr18:28640436..28642394,2	K562	blood:
3	chr18:28640728..28642575-chr18:28644774..28647318,2	K562	blood:
4	chr18:28635379..28636910-chr18:28640103..28642394,2	K562	blood:
5	chr18:28640333..28642657-chr18:28648234..28652025,3	K562	blood:

Variant related genes	Relation type
ENSG00000261521	TF binding region

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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1789037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1789055	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866104	0.85[ASN][1000 genomes]
rs2019624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[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
rs1790694	DSC3	Cis_1M	lymphoblastoid	RTeQTL
rs1790694	FAM59A	cis	parietal	SCAN
rs1790694	DSC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28636400-28645000	Weak transcription	Fetal Intestine Large	intestine
2	chr18:28636600-28644800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr18:28636600-28645200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr18:28637000-28643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr18:28637000-28645000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr18:28637000-28647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr18:28637200-28649000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr18:28638000-28647400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr18:28638200-28649000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:28638400-28645400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr18:28639000-28647400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr18:28639200-28647600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr18:28639200-28648600	Weak transcription	Pancreas	Pancrea
14	chr18:28639400-28646800	Weak transcription	HepG2	liver
15	chr18:28640600-28642400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr18:28640600-28648000	Weak transcription	Left Ventricle	heart
17	chr18:28640600-28648800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr18:28640800-28680400	Weak transcription	Right Ventricle	heart
19	chr18:28641000-28643000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr18:28641200-28642800	Enhancers	Primary hematopoietic stem cells	blood
21	chr18:28641600-28642200	Enhancers	GM12878-XiMat	blood
22	chr18:28641600-28642800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr18:28641600-28642800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr18:28641800-28642200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr18:28641800-28642200	Enhancers	Fetal Heart	heart
26	chr18:28641800-28642800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr18:28641800-28642800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:28642000-28642200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr18:28642000-28642200	Enhancers	HMEC	breast

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