Variant report

Variant	rs9947401
Chromosome Location	chr18:29105117-29105118
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: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1042769	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10502571	0.85[CHD][hapmap]
rs11661247	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs12326068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449077	0.99[EUR][1000 genomes]
rs1626261	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1667212	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1667213	0.90[CEU][hapmap];0.99[EUR][1000 genomes]
rs1791174	0.85[EUR][1000 genomes]
rs1941939	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2096919	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2276150	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704039	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2704041	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2848664	1.00[EUR][1000 genomes]
rs28522238	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506931	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7232391	0.96[ASN][1000 genomes]
rs8084771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8093731	0.85[CHD][hapmap]
rs9304100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949695	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9949790	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951860	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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
rs9947401	DSG2	Cis_1M	lymphoblastoid	RTeQTL

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	chr18:29094000-29110400	Weak transcription	Esophagus	oesophagus
3	chr18:29094000-29118800	Weak transcription	Gastric	stomach
4	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
5	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr18:29097000-29116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:29097000-29118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr18:29097200-29118400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
11	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:29098000-29115400	Weak transcription	Fetal Stomach	stomach
14	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr18:29099200-29108400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr18:29099400-29113600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr18:29099600-29105800	Strong transcription	HepG2	liver
21	chr18:29099600-29108000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr18:29099600-29109000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr18:29099600-29109000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr18:29099800-29106000	Strong transcription	Fetal Intestine Large	intestine
27	chr18:29099800-29107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr18:29099800-29108400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr18:29099800-29108600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:29099800-29113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:29100000-29112600	Strong transcription	HMEC	breast
32	chr18:29100200-29108800	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr18:29100400-29105800	Strong transcription	Liver	Liver
34	chr18:29101000-29105400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
36	chr18:29101800-29116000	Weak transcription	A549	lung
37	chr18:29102000-29116000	Weak transcription	Placenta	Placenta
38	chr18:29102400-29116000	Weak transcription	Fetal Lung	lung
39	chr18:29102400-29118400	Weak transcription	Thymus	Thymus
40	chr18:29103000-29106000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr18:29103200-29105400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr18:29103400-29105200	Strong transcription	K562	blood
43	chr18:29103400-29108200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr18:29103400-29108600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr18:29103600-29105600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr18:29103600-29106600	Strong transcription	Adipose Nuclei	Adipose
48	chr18:29103800-29105400	Strong transcription	Left Ventricle	heart
49	chr18:29103800-29105800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr18:29103800-29107200	Strong transcription	NH-A	brain

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