Variant report

Variant	rs3742355
Chromosome Location	chr14:39486040-39486041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10134654	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10137988	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10140341	0.92[ASN][1000 genomes]
rs10141471	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11157041	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434847	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12437031	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12437346	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12878789	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12879229	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883061	0.92[ASN][1000 genomes]
rs12885242	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890771	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1555257	0.96[ASN][1000 genomes]
rs17108728	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2415524	0.95[ASN][1000 genomes]
rs28367031	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28502115	0.94[ASN][1000 genomes]
rs28699217	0.89[ASN][1000 genomes]
rs28810420	0.94[ASN][1000 genomes]
rs34642409	0.80[ASN][1000 genomes]
rs34676226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34985331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35224434	0.80[ASN][1000 genomes]
rs35287240	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35423721	0.94[ASN][1000 genomes]
rs35712728	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35807641	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35992529	0.94[ASN][1000 genomes]
rs36161173	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742354	0.94[ASN][1000 genomes]
rs4902259	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902308	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571893	0.94[ASN][1000 genomes]
rs71407775	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152746	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322992	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975521	0.92[AMR][1000 genomes];0.86[EUR][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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3742355	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39463600-39495200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr14:39464800-39492600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:39465600-39498200	Weak transcription	NH-A	brain
4	chr14:39469200-39497400	Weak transcription	HSMM	muscle
5	chr14:39473400-39498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:39479000-39493000	Weak transcription	A549	lung
7	chr14:39479600-39498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:39479800-39492800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:39480200-39499000	Weak transcription	NHDF-Ad	bronchial
10	chr14:39481200-39486400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr14:39481200-39492600	Weak transcription	Fetal Intestine Small	intestine
12	chr14:39482200-39495000	Weak transcription	HUVEC	blood vessel
13	chr14:39482800-39499200	Weak transcription	Right Ventricle	heart
14	chr14:39483000-39486400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:39483600-39486400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:39483800-39492600	Weak transcription	Osteobl	bone
17	chr14:39484800-39486800	Enhancers	Liver	Liver
18	chr14:39485200-39486200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr14:39485200-39498600	Weak transcription	Aorta	Aorta
20	chr14:39485400-39486200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr14:39485400-39486400	Strong transcription	HSMMtube	muscle
22	chr14:39485600-39486200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:39485600-39486200	Enhancers	Stomach Mucosa	stomach
24	chr14:39485600-39487000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr14:39485800-39486200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr14:39485800-39487200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr14:39485800-39487200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr14:39486000-39486200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr14:39486000-39486200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr14:39486000-39486200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:39486000-39486400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:39486000-39486600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:39486000-39486600	Enhancers	Fetal Intestine Large	intestine
34	chr14:39486000-39487000	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr14:39486000-39487000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr14:39486000-39487000	Flanking Active TSS	HepG2	liver
37	chr14:39486000-39487200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr14:39486000-39487200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr14:39486000-39487200	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr14:39486000-39498600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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