Variant report

Variant	rs2230233
Chromosome Location	chr18:29104698-29104699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29098189..29101114-chr18:29103613..29106437,2	MCF-7	breast:
2	chr18:29089902..29091907-chr18:29103774..29106283,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1047433	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs1449078	0.96[EUR][1000 genomes]
rs1667216	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1667218	0.96[EUR][1000 genomes]
rs1791173	0.96[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs1791176	0.81[EUR][1000 genomes]
rs1791230	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1791233	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs1791235	0.96[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs1941938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2155948	0.80[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs2256638	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2276149	0.96[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs2595364	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2704038	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2704042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376849	0.87[EUR][1000 genomes]
rs3108921	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132910	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243604	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][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	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2230233	DSG4	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29092000-29115600	Weak transcription	GM12878-XiMat	blood
2	chr18:29094000-29104800	Weak transcription	Ovary	ovary
3	chr18:29094000-29104800	Weak transcription	Pancreas	Pancrea
4	chr18:29094000-29110400	Weak transcription	Esophagus	oesophagus
5	chr18:29094000-29118800	Weak transcription	Gastric	stomach
6	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
7	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr18:29097000-29116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:29097000-29118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:29097200-29105000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:29097200-29118400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
14	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr18:29098000-29115400	Weak transcription	Fetal Stomach	stomach
17	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr18:29099200-29108400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr18:29099400-29113600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr18:29099600-29105800	Strong transcription	HepG2	liver
24	chr18:29099600-29108000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:29099600-29109000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr18:29099600-29109000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:29099800-29106000	Strong transcription	Fetal Intestine Large	intestine
30	chr18:29099800-29107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr18:29099800-29108400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr18:29099800-29108600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:29099800-29113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr18:29100000-29112600	Strong transcription	HMEC	breast
35	chr18:29100200-29108800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr18:29100400-29105800	Strong transcription	Liver	Liver
37	chr18:29101000-29105400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
39	chr18:29101800-29116000	Weak transcription	A549	lung
40	chr18:29102000-29116000	Weak transcription	Placenta	Placenta
41	chr18:29102400-29116000	Weak transcription	Fetal Lung	lung
42	chr18:29102400-29118400	Weak transcription	Thymus	Thymus
43	chr18:29103000-29106000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:29103200-29105400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr18:29103400-29105200	Strong transcription	K562	blood
46	chr18:29103400-29108200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr18:29103400-29108600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr18:29103600-29105600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr18:29103600-29106600	Strong transcription	Adipose Nuclei	Adipose

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