Variant report

Variant	rs12899800
Chromosome Location	chr15:79159730-79159731
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10851913	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10851914	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12592340	0.84[AMR][1000 genomes]
rs12595538	0.81[ASN][1000 genomes]
rs12898532	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12911969	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59772922	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6495346	0.84[ASN][1000 genomes]
rs7171258	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7180375	0.84[ASN][1000 genomes]
rs7181033	0.81[ASN][1000 genomes]
rs734287	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7402286	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8042186	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs892787	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9806693	0.93[AMR][1000 genomes];0.91[ASN][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12899800	CTSH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79153000-79163200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:79153200-79163200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:79153200-79164600	Weak transcription	A549	lung
4	chr15:79156800-79164400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:79157200-79163400	Weak transcription	HepG2	liver

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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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