Variant report

Variant	rs12903205
Chromosome Location	chr15:75170082-75170083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75167898..75170533-chr15:75183102..75184983,2	K562	blood:
2	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:

Variant related genes	Relation type
ENSG00000178802	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11072511	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072512	0.94[EUR][1000 genomes]
rs11072513	0.82[EUR][1000 genomes]
rs11072514	0.85[EUR][1000 genomes]
rs1127796	0.95[EUR][1000 genomes]
rs1130741	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1133322	0.92[EUR][1000 genomes]
rs1133323	0.84[EUR][1000 genomes]
rs11630918	0.87[EUR][1000 genomes]
rs11633472	0.87[EUR][1000 genomes]
rs11638130	0.86[EUR][1000 genomes]
rs11854704	0.90[EUR][1000 genomes]
rs11856413	0.86[EUR][1000 genomes]
rs11857695	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12441499	0.83[AFR][1000 genomes]
rs12898539	0.87[EUR][1000 genomes]
rs12899430	0.87[EUR][1000 genomes]
rs12899787	0.92[EUR][1000 genomes]
rs12900662	0.96[EUR][1000 genomes]
rs12901190	0.84[EUR][1000 genomes]
rs12902515	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12903370	0.85[EUR][1000 genomes]
rs12904326	0.85[EUR][1000 genomes]
rs12904897	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12907898	0.93[EUR][1000 genomes]
rs12908365	0.91[EUR][1000 genomes]
rs12909335	0.85[EUR][1000 genomes]
rs12911254	0.89[EUR][1000 genomes]
rs12912839	0.85[EUR][1000 genomes]
rs12913293	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12914217	0.82[EUR][1000 genomes]
rs2044157	0.83[EUR][1000 genomes]
rs3935818	0.82[AFR][1000 genomes]
rs4643278	0.96[EUR][1000 genomes]
rs4886608	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886632	1.00[EUR][1000 genomes]
rs4886636	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886639	0.86[EUR][1000 genomes]
rs56671860	0.83[AFR][1000 genomes]
rs59945415	0.92[EUR][1000 genomes]
rs60494786	0.83[AFR][1000 genomes]
rs62029167	0.93[EUR][1000 genomes]
rs7179093	0.82[AFR][1000 genomes]
rs729263	0.83[AFR][1000 genomes]
rs7495664	0.85[EUR][1000 genomes]
rs7495739	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7497026	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7497393	0.90[EUR][1000 genomes]
rs8025447	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9672491	0.83[AFR][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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12903205	SCAMP5	cis	Artery Tibial	GTEx
rs12903205	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12903205	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12903205	SCAMP2	cis	Whole Blood	GTEx
rs12903205	SCAMP2	cis	Esophagus Mucosa	GTEx
rs12903205	ULK3	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75166200-75181000	Weak transcription	Fetal Heart	heart
2	chr15:75166400-75174200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:75166600-75176400	Weak transcription	A549	lung
4	chr15:75169000-75174600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links