Variant report

Variant	rs4121653
Chromosome Location	chr18:29846411-29846412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16962940	0.92[CEU][hapmap]
rs16962953	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs16962977	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs3859366	0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs60291556	0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4121653	DSG3	cis	parietal	SCAN
rs4121653	KLHL14	cis	cerebellum	SCAN

Chromatin state (count:58 , 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	chr18:29838800-29846800	Weak transcription	Liver	Liver
14	chr18:29838800-29846800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:29839000-29847600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr18:29839000-29847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr18:29839200-29847600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
19	chr18:29840000-29847800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr18:29841000-29847800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:29842600-29847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr18:29842800-29848000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:29843000-29867000	Weak transcription	Brain Angular Gyrus	brain
24	chr18:29843200-29847800	Weak transcription	Fetal Muscle Leg	muscle
25	chr18:29843400-29847600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr18:29843400-29847800	Weak transcription	Brain Anterior Caudate	brain
27	chr18:29843400-29848000	Weak transcription	Ovary	ovary
28	chr18:29843600-29847600	Weak transcription	Brain Substantia Nigra	brain
29	chr18:29844000-29847600	Weak transcription	Gastric	stomach
30	chr18:29844200-29847400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr18:29844200-29848600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr18:29844400-29847000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr18:29844800-29847600	Weak transcription	Fetal Kidney	kidney
34	chr18:29844800-29848200	Weak transcription	Fetal Brain Female	brain
35	chr18:29845000-29847400	Weak transcription	Fetal Lung	lung
36	chr18:29845000-29848000	Weak transcription	Fetal Intestine Small	intestine
37	chr18:29845200-29846800	Weak transcription	Fetal Intestine Large	intestine
38	chr18:29845200-29852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr18:29845200-29857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr18:29845400-29848000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr18:29845400-29850200	Strong transcription	Adipose Nuclei	Adipose
42	chr18:29845400-29851800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr18:29845600-29848000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr18:29845800-29847400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr18:29846000-29847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr18:29846000-29847600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr18:29846000-29847600	Weak transcription	Fetal Stomach	stomach
48	chr18:29846000-29847600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr18:29846000-29847600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr18:29846000-29867000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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