Variant report

Variant	rs3737375
Chromosome Location	chr18:29104204-29104205
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:
2	chr18:29089902..29091907-chr18:29103774..29106283,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10163532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10502573	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11542765	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12327220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12604517	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12605787	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12607843	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12607944	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1375443	0.97[EUR][1000 genomes]
rs16962075	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16962077	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17802774	0.93[EUR][1000 genomes]
rs1791155	0.94[EUR][1000 genomes]
rs2053825	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2053826	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2053827	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2096918	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]
rs2256638	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2276149	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs2278792	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2290128	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2290129	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3737378	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829628	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4470222	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4471764	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55899143	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56389431	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62095191	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62095194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095195	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095223	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095226	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7244098	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7506013	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807377	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9807379	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[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
rs3737375	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	chr18:29094000-29104400	Weak transcription	Fetal Heart	heart
3	chr18:29094000-29104800	Weak transcription	Ovary	ovary
4	chr18:29094000-29104800	Weak transcription	Pancreas	Pancrea
5	chr18:29094000-29110400	Weak transcription	Esophagus	oesophagus
6	chr18:29094000-29118800	Weak transcription	Gastric	stomach
7	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
8	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:29097000-29116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:29097000-29118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:29097200-29105000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr18:29097200-29118400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
15	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:29098000-29115400	Weak transcription	Fetal Stomach	stomach
18	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:29099200-29108400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr18:29099400-29113600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr18:29099600-29105800	Strong transcription	HepG2	liver
25	chr18:29099600-29108000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:29099600-29109000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr18:29099600-29109000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:29099800-29106000	Strong transcription	Fetal Intestine Large	intestine
31	chr18:29099800-29107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr18:29099800-29108400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr18:29099800-29108600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr18:29099800-29113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr18:29100000-29112600	Strong transcription	HMEC	breast
36	chr18:29100200-29104600	Strong transcription	Hela-S3	cervix
37	chr18:29100200-29108800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr18:29100400-29105800	Strong transcription	Liver	Liver
39	chr18:29101000-29105400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
41	chr18:29101800-29116000	Weak transcription	A549	lung
42	chr18:29102000-29116000	Weak transcription	Placenta	Placenta
43	chr18:29102400-29116000	Weak transcription	Fetal Lung	lung
44	chr18:29102400-29118400	Weak transcription	Thymus	Thymus
45	chr18:29103000-29106000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr18:29103200-29105400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr18:29103400-29105200	Strong transcription	K562	blood
48	chr18:29103400-29108200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr18:29103400-29108600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum

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