Variant report

Variant	rs1941939
Chromosome Location	chr18:29109642-29109643
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1042769	0.90[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11661247	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs12326068	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1449077	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1626261	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1667212	0.90[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1667213	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1791174	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276150	0.90[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2704039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2704041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2848664	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28522238	1.00[EUR][1000 genomes]
rs6506931	0.99[EUR][1000 genomes]
rs8084771	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9304100	0.90[EUR][1000 genomes]
rs9304101	0.99[EUR][1000 genomes]
rs9947401	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs9949695	0.97[EUR][1000 genomes]
rs9949790	0.97[EUR][1000 genomes]
rs9951860	1.00[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
rs1941939	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	chr18:29099400-29113600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr18:29099800-29113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr18:29100000-29112600	Strong transcription	HMEC	breast
23	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
24	chr18:29101800-29116000	Weak transcription	A549	lung
25	chr18:29102000-29116000	Weak transcription	Placenta	Placenta
26	chr18:29102400-29116000	Weak transcription	Fetal Lung	lung
27	chr18:29102400-29118400	Weak transcription	Thymus	Thymus
28	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr18:29103800-29114200	Weak transcription	Primary T cells from cord blood	blood
30	chr18:29104000-29116200	Weak transcription	Fetal Kidney	kidney
31	chr18:29104200-29118400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr18:29105200-29127600	Weak transcription	Fetal Heart	heart
33	chr18:29105400-29116200	Weak transcription	Left Ventricle	heart
34	chr18:29105400-29119200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr18:29105400-29119200	Weak transcription	Pancreas	Pancrea
36	chr18:29105400-29120200	Weak transcription	Colonic Mucosa	Colon
37	chr18:29105600-29111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr18:29105600-29111000	Weak transcription	Ovary	ovary
39	chr18:29105600-29116200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr18:29105800-29110400	Weak transcription	HepG2	liver
41	chr18:29105800-29111000	Weak transcription	Liver	Liver
42	chr18:29105800-29111400	Weak transcription	Fetal Thymus	thymus
43	chr18:29105800-29116200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr18:29106200-29113000	Weak transcription	Fetal Intestine Small	intestine
45	chr18:29106600-29116200	Weak transcription	Adipose Nuclei	Adipose
46	chr18:29106800-29110600	Weak transcription	Hela-S3	cervix
47	chr18:29106800-29111000	Weak transcription	K562	blood
48	chr18:29106800-29116600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr18:29107200-29120800	Weak transcription	NH-A	brain
50	chr18:29107800-29111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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