Variant report

Variant	rs718780
Chromosome Location	chr18:29255261-29255262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10048377	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10775449	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11081706	0.85[YRI][hapmap]
rs11081707	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081708	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11660271	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11664177	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12327203	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12605321	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12964693	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449082	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1551006	0.83[ASW][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1614197	0.96[EUR][1000 genomes]
rs17661533	1.00[YRI][hapmap]
rs1979105	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs34530749	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4799589	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs8098191	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968325	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[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	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs718780	CDH2	cis	cerebellum	SCAN
rs718780	DSC1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29235600-29257800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:29239600-29258000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr18:29244600-29255400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr18:29244600-29257600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:29250200-29258000	Weak transcription	Small Intestine	intestine
6	chr18:29253000-29255400	Weak transcription	Stomach Mucosa	stomach
7	chr18:29253000-29255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr18:29253000-29256200	Enhancers	Primary hematopoietic stem cells	blood
9	chr18:29253000-29257600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr18:29253200-29257800	Weak transcription	Fetal Thymus	thymus
11	chr18:29253200-29258600	Weak transcription	Osteobl	bone
12	chr18:29253200-29258800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr18:29253200-29262800	Weak transcription	HepG2	liver
14	chr18:29253400-29257400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr18:29253400-29257400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:29253400-29258600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:29253400-29258600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr18:29253400-29258600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr18:29253400-29258800	Weak transcription	Adipose Nuclei	Adipose
20	chr18:29253400-29259400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr18:29253400-29259800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr18:29253400-29260000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:29253600-29257800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr18:29253600-29257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr18:29253600-29257800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr18:29253600-29257800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr18:29253600-29258000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:29253600-29258200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr18:29253600-29258200	Weak transcription	NHEK	skin
30	chr18:29253600-29260400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr18:29253600-29262200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:29253600-29264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr18:29253800-29257400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr18:29253800-29257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:29253800-29257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:29254000-29257600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr18:29254000-29257800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr18:29254200-29257600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr18:29254600-29258000	Weak transcription	HMEC	breast
40	chr18:29254800-29258800	Enhancers	HUVEC	blood vessel
41	chr18:29255000-29255600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr18:29255000-29255600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr18:29255000-29256800	Enhancers	Duodenum Mucosa	Duodenum
44	chr18:29255200-29255600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr18:29255200-29255600	Enhancers	Fetal Intestine Small	intestine
46	chr18:29255200-29255600	Enhancers	Fetal Lung	lung
47	chr18:29255200-29255600	Flanking Active TSS	GM12878-XiMat	blood
48	chr18:29255200-29256200	Enhancers	Fetal Intestine Large	intestine
49	chr18:29255200-29257800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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