Variant report

Variant	rs10054780
Chromosome Location	chr5:128107742-128107743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1035407	1.00[CHB][hapmap]
rs1422443	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1603409	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs173520	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs189687	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2012809	1.00[CHB][hapmap]
rs2079100	0.85[MEX][hapmap]
rs247095	0.84[ASN][1000 genomes]
rs247097	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247099	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247100	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247180	0.86[EUR][1000 genomes]
rs247209	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2545018	0.85[MEX][hapmap]
rs2577469	1.00[LWK][hapmap];0.85[MEX][hapmap]
rs4835959	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4836402	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6595859	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[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	nsv1023405	chr5:127955360-128190069	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv882836	chr5:127999225-128136519	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10054780	ALDH7A1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128104000-128113600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:128106800-128109000	Weak transcription	HUVEC	blood vessel
3	chr5:128107000-128109200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:128107000-128110400	Weak transcription	Fetal Lung	lung
5	chr5:128107400-128109400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:128107600-128108200	Enhancers	Brain Substantia Nigra	brain

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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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