Variant report

Variant	rs7154078
Chromosome Location	chr14:78785123-78785124
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10149483	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11159349	0.89[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs1882813	0.89[CHB][hapmap];0.97[CHD][hapmap]
rs1882814	0.89[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs4903750	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs61976036	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7150775	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs7153365	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7153993	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7155434	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs8013890	0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1054051	chr14:78772614-78805311	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7154078	ALKBH1	cis	parietal	SCAN
rs7154078	YLPM1	cis	parietal	SCAN
rs7154078	VASH1	cis	cerebellum	SCAN
rs7154078	GTF2A1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78779200-78787000	Enhancers	Brain Germinal Matrix	brain
2	chr14:78779400-78786000	Weak transcription	Brain Anterior Caudate	brain
3	chr14:78783200-78785200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr14:78783200-78794000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:78783400-78785600	Weak transcription	Brain Substantia Nigra	brain
6	chr14:78783400-78786000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr14:78783600-78785600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:78783600-78786200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr14:78783800-78785400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:78783800-78786200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr14:78784800-78786400	Enhancers	K562	blood

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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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