Variant report

Variant	rs669116
Chromosome Location	chr18:29846914-29846915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1614242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs470958	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596653	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs606576	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs613616	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs613941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618862	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs624130	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap]
rs624171	0.95[CEU][hapmap]
rs625863	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs635901	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.98[ASN][1000 genomes]
rs636809	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs638664	0.81[GIH][hapmap]
rs645526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs646452	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs647499	0.94[ASN][1000 genomes]
rs676968	0.81[GIH][hapmap]
rs683375	0.97[ASN][1000 genomes]
rs9510	0.95[CEU][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs669116	DSG3	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29823800-29848000	Weak transcription	Aorta	Aorta
2	chr18:29831400-29847600	Weak transcription	Pancreas	Pancrea
3	chr18:29835200-29861600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:29837400-29847800	Weak transcription	Right Ventricle	heart
5	chr18:29837400-29867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:29837600-29848200	Weak transcription	Colonic Mucosa	Colon
7	chr18:29838000-29847600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:29838000-29848000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:29838400-29847600	Weak transcription	Brain Hippocampus Middle	brain
10	chr18:29838600-29848000	Weak transcription	HepG2	liver
11	chr18:29838600-29851400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:29838600-29851600	Weak transcription	Stomach Mucosa	stomach
13	chr18:29839000-29847600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr18:29839000-29847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr18:29839200-29847600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
17	chr18:29840000-29847800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr18:29841000-29847800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:29842600-29847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr18:29842800-29848000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr18:29843000-29867000	Weak transcription	Brain Angular Gyrus	brain
22	chr18:29843200-29847800	Weak transcription	Fetal Muscle Leg	muscle
23	chr18:29843400-29847600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr18:29843400-29847800	Weak transcription	Brain Anterior Caudate	brain
25	chr18:29843400-29848000	Weak transcription	Ovary	ovary
26	chr18:29843600-29847600	Weak transcription	Brain Substantia Nigra	brain
27	chr18:29844000-29847600	Weak transcription	Gastric	stomach
28	chr18:29844200-29847400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr18:29844200-29848600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr18:29844400-29847000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr18:29844800-29847600	Weak transcription	Fetal Kidney	kidney
32	chr18:29844800-29848200	Weak transcription	Fetal Brain Female	brain
33	chr18:29845000-29847400	Weak transcription	Fetal Lung	lung
34	chr18:29845000-29848000	Weak transcription	Fetal Intestine Small	intestine
35	chr18:29845200-29852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr18:29845200-29857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr18:29845400-29848000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:29845400-29850200	Strong transcription	Adipose Nuclei	Adipose
39	chr18:29845400-29851800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr18:29845600-29848000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:29845800-29847400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr18:29846000-29847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr18:29846000-29847600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr18:29846000-29847600	Weak transcription	Fetal Stomach	stomach
45	chr18:29846000-29847600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr18:29846000-29847600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr18:29846000-29867000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr18:29846200-29848000	Weak transcription	Lung	lung
49	chr18:29846200-29850400	Weak transcription	Placenta	Placenta
50	chr18:29846200-29850600	Strong transcription	Brain Inferior Temporal Lobe	brain

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