Variant report

Variant	rs10148623
Chromosome Location	chr14:39464408-39464409
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10133362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10134654	0.84[EUR][1000 genomes]
rs10137988	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[EUR][1000 genomes]
rs10141471	0.82[EUR][1000 genomes]
rs1061583	1.00[ASW][hapmap]
rs12147991	1.00[ASW][hapmap]
rs12164875	0.82[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12437031	0.83[EUR][1000 genomes]
rs12437346	0.81[EUR][1000 genomes]
rs12878789	0.82[EUR][1000 genomes]
rs12885242	1.00[ASW][hapmap]
rs12889064	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12890771	1.00[ASW][hapmap];0.84[EUR][1000 genomes]
rs17108728	0.82[EUR][1000 genomes]
rs17108846	1.00[ASW][hapmap]
rs17677562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003740	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28367031	0.81[EUR][1000 genomes]
rs34673321	0.81[ASN][1000 genomes]
rs34702834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34875314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35287240	0.81[EUR][1000 genomes]
rs3742354	1.00[ASW][hapmap]
rs4899137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902418	1.00[ASW][hapmap]
rs532	0.86[CHB][hapmap]
rs8018842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8019028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs975521	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10148623	MIA2	cis	parietal	SCAN
rs10148623	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39450000-39465000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr14:39455600-39464800	Weak transcription	Psoas Muscle	Psoas
3	chr14:39455800-39465200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr14:39458400-39465000	Enhancers	HUVEC	blood vessel
5	chr14:39459000-39464800	Weak transcription	Right Atrium	heart
6	chr14:39459600-39464600	Weak transcription	Left Ventricle	heart
7	chr14:39459600-39469000	Weak transcription	Stomach Mucosa	stomach
8	chr14:39462200-39480400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:39462800-39465000	Enhancers	Fetal Lung	lung
10	chr14:39463000-39464600	Weak transcription	Adipose Nuclei	Adipose
11	chr14:39463200-39465200	Enhancers	Fetal Stomach	stomach
12	chr14:39463600-39464800	Enhancers	Brain Hippocampus Middle	brain
13	chr14:39463600-39476000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:39463600-39495200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr14:39463800-39464800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr14:39463800-39465000	Enhancers	Brain Anterior Caudate	brain
17	chr14:39463800-39465000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr14:39463800-39465200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr14:39463800-39465200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr14:39463800-39473200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:39464200-39465000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr14:39464200-39483000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:39464400-39468800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr14:39464400-39469000	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links