Variant report

Variant	rs4799310
Chromosome Location	chr18:29088709-29088710
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1350731	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1460602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17660585	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1824477	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1841396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2212617	0.91[ASN][1000 genomes]
rs2212618	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2219584	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2704050	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704051	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704052	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2704053	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2704055	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2848677	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848680	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848681	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4799573	0.98[ASN][1000 genomes]
rs6506927	0.94[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6506928	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7227343	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7227984	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7231288	0.96[ASN][1000 genomes]
rs7231553	0.96[ASN][1000 genomes]
rs7232282	0.98[ASN][1000 genomes]
rs7235272	0.96[ASN][1000 genomes]
rs7236324	0.98[ASN][1000 genomes]
rs7236469	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7238729	0.98[ASN][1000 genomes]
rs7239805	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7240824	0.83[ASN][1000 genomes]
rs7240920	0.90[ASN][1000 genomes]
rs7241107	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73414280	0.97[ASN][1000 genomes]
rs73953901	0.98[ASN][1000 genomes]
rs9304097	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304098	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304099	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941421	0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9945031	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9945420	0.88[ASN][1000 genomes]
rs9951843	0.93[ASN][1000 genomes]
rs9961910	0.94[ASN][1000 genomes]
rs9961920	0.98[ASN][1000 genomes]
rs9961925	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9962121	0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs9962318	0.98[ASN][1000 genomes]
rs9962333	0.88[ASN][1000 genomes]
rs9962423	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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
rs4799310	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29080400-29091000	Weak transcription	Colonic Mucosa	Colon
2	chr18:29080600-29088800	Weak transcription	A549	lung
3	chr18:29080600-29089600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:29080600-29093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:29080600-29100000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr18:29080600-29100400	Weak transcription	Fetal Thymus	thymus
7	chr18:29080800-29092400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr18:29081000-29091400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:29081600-29092000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:29081600-29092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr18:29081600-29092200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr18:29081600-29093200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr18:29081800-29092200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr18:29083400-29092600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:29084000-29090600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr18:29084800-29091000	Weak transcription	Left Ventricle	heart
17	chr18:29084800-29093600	Weak transcription	Gastric	stomach
18	chr18:29085200-29090600	Weak transcription	Fetal Intestine Small	intestine
19	chr18:29085200-29091000	Weak transcription	Right Atrium	heart
20	chr18:29085400-29089600	Weak transcription	Stomach Mucosa	stomach
21	chr18:29085400-29090800	Weak transcription	Pancreas	Pancrea
22	chr18:29085400-29090800	Weak transcription	K562	blood
23	chr18:29086200-29089600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr18:29086200-29089600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr18:29086400-29090800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr18:29086400-29091600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr18:29086600-29090000	Weak transcription	Fetal Intestine Large	intestine
28	chr18:29087200-29096200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:29088000-29094200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:29088400-29088800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr18:29088400-29093200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr18:29088600-29089200	Enhancers	Fetal Heart	heart
33	chr18:29088600-29089200	Enhancers	Hela-S3	cervix
34	chr18:29088600-29092000	Enhancers	GM12878-XiMat	blood
35	chr18:29088600-29093200	Enhancers	NHEK	skin
36	chr18:29088600-29093400	Enhancers	HMEC	breast
37	chr18:29088600-29094400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr18:29088600-29094400	Enhancers	HepG2	liver
39	chr18:29088600-29094600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr18:29088600-29095000	Enhancers	Placenta Amnion	Placenta Amnion

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