Variant report

Variant	rs2276149
Chromosome Location	chr18:29098323-29098324
allele	A/G
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:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10163532	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs1047433	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs12327220	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs1449078	0.88[EUR][1000 genomes]
rs1667216	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs1667218	0.89[EUR][1000 genomes]
rs1791173	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs1791230	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs1791233	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1791235	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs1941938	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2096918	0.85[CHB][hapmap]
rs2155948	0.81[EUR][1000 genomes]
rs2230233	0.96[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs2595364	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2704038	0.94[EUR][1000 genomes]
rs2704042	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs28376849	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3108921	0.91[EUR][1000 genomes]
rs3132910	0.91[EUR][1000 genomes]
rs3737375	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs7243604	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs9807377	0.82[ASN][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
rs2276149	DSG4	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29080600-29100000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:29080600-29100400	Weak transcription	Fetal Thymus	thymus
3	chr18:29091400-29103800	Weak transcription	Left Ventricle	heart
4	chr18:29092000-29115600	Weak transcription	GM12878-XiMat	blood
5	chr18:29092400-29100400	Weak transcription	Liver	Liver
6	chr18:29092800-29104200	Weak transcription	Colonic Mucosa	Colon
7	chr18:29093000-29100600	Weak transcription	Stomach Mucosa	stomach
8	chr18:29093200-29099800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr18:29093400-29101000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr18:29093400-29103000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:29093600-29099600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr18:29094000-29098600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr18:29094000-29099400	Weak transcription	K562	blood
14	chr18:29094000-29099600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr18:29094000-29101000	Weak transcription	Placenta	Placenta
16	chr18:29094000-29103600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr18:29094000-29103800	Weak transcription	NH-A	brain
18	chr18:29094000-29104000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr18:29094000-29104400	Weak transcription	Fetal Heart	heart
20	chr18:29094000-29104800	Weak transcription	Ovary	ovary
21	chr18:29094000-29104800	Weak transcription	Pancreas	Pancrea
22	chr18:29094000-29110400	Weak transcription	Esophagus	oesophagus
23	chr18:29094000-29118800	Weak transcription	Gastric	stomach
24	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
25	chr18:29094200-29099800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr18:29094400-29099400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:29094400-29099600	Weak transcription	HepG2	liver
28	chr18:29094400-29100000	Weak transcription	HMEC	breast
29	chr18:29094400-29100200	Weak transcription	Hela-S3	cervix
30	chr18:29094600-29099800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr18:29094600-29099800	Weak transcription	Fetal Intestine Large	intestine
32	chr18:29094600-29099800	Weak transcription	A549	lung
33	chr18:29094800-29099600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr18:29096200-29098600	Strong transcription	NHEK	skin
35	chr18:29096800-29099200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr18:29096800-29099400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:29096800-29099400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr18:29096800-29100200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr18:29096800-29103600	Weak transcription	Adipose Nuclei	Adipose
40	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr18:29097000-29099800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr18:29097000-29099800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr18:29097000-29101000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr18:29097000-29103200	Weak transcription	Fetal Intestine Small	intestine
46	chr18:29097000-29116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:29097000-29118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:29097200-29099600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr18:29097200-29101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr18:29097200-29105000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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