Variant report

Variant	rs13154048
Chromosome Location	chr5:116500367-116500368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10068492	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10223221	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13166199	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13167829	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13168914	0.94[EUR][1000 genomes]
rs13169066	0.94[EUR][1000 genomes]
rs13183692	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361759	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1389932	1.00[ASN][1000 genomes]
rs17393052	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4920964	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6892426	0.93[ASN][1000 genomes]

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	esv2752839	chr5:116461101-116504101	Enhancers Weak transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13154048	SEMA6A	cis	cerebellum	SCAN
rs13154048	AQPEP	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116494400-116501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:116498000-116501800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:116498000-116502200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:116498400-116500800	Weak transcription	Brain Substantia Nigra	brain
5	chr5:116499800-116501400	Weak transcription	Brain Anterior Caudate	brain
6	chr5:116500000-116501600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:116500200-116500400	Enhancers	Brain Hippocampus Middle	brain
8	chr5:116500200-116501400	Enhancers	Brain Inferior Temporal Lobe	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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