Variant report

Variant	rs12883643
Chromosome Location	chr14:78770121-78770122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17107186	0.85[JPT][hapmap]
rs17754913	0.85[JPT][hapmap]
rs17754986	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs17755066	0.82[CEU][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs17827951	0.85[JPT][hapmap]
rs17827963	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs17828054	0.82[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs2365680	0.82[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs34757401	0.97[ASN][1000 genomes]
rs35018455	0.97[ASN][1000 genomes]
rs35471648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4903736	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.88[AMR][1000 genomes]
rs4903741	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4903749	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7148695	0.85[JPT][hapmap]
rs7158061	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8006711	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8008429	0.81[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832837	chr14:78766805-78946526	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12883643	GTF2A1	cis	cerebellum	SCAN
rs12883643	JDP2	cis	cerebellum	SCAN
rs12883643	PNMA1	cis	parietal	SCAN
rs12883643	PTGR2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78738600-78778200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr14:78738600-78779000	Weak transcription	Brain Angular Gyrus	brain
3	chr14:78750200-78778400	Weak transcription	Brain Anterior Caudate	brain
4	chr14:78765400-78771200	Weak transcription	Fetal Brain Male	brain
5	chr14:78769000-78774000	Enhancers	Brain Germinal Matrix	brain
6	chr14:78769200-78783200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:78769800-78773800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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Input of quick search could be:

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

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