Variant report

Variant	rs2003740
Chromosome Location	chr14:39473295-39473296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10133362	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10134654	0.82[EUR][1000 genomes]
rs10137988	0.82[EUR][1000 genomes]
rs10141471	0.83[EUR][1000 genomes]
rs10148623	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12164875	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs12437031	0.81[EUR][1000 genomes]
rs12878789	0.80[EUR][1000 genomes]
rs12889064	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12890771	0.82[EUR][1000 genomes]
rs17108728	0.83[EUR][1000 genomes]
rs17677562	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34702834	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34875314	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899137	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902285	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532	0.86[CHB][hapmap]
rs8018842	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8019028	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	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
4	esv3427572	chr14:39473219-39473760	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2003740	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39462200-39480400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr14:39463600-39476000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:39463600-39495200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr14:39464200-39483000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr14:39464800-39492600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:39465000-39473800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr14:39465600-39498200	Weak transcription	NH-A	brain
8	chr14:39466000-39481000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr14:39466000-39483000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr14:39469200-39497400	Weak transcription	HSMM	muscle
11	chr14:39469600-39473400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr14:39470600-39474000	Active TSS	Right Atrium	heart
13	chr14:39473000-39473800	Active TSS	Adipose Nuclei	Adipose
14	chr14:39473200-39473400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:39473200-39473400	Flanking Active TSS	Left Ventricle	heart
16	chr14:39473200-39473600	Enhancers	Right Ventricle	heart
17	chr14:39473200-39474800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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