Variant report

Variant	rs55877218
Chromosome Location	chr15:75282541-75282542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75274624..75277019-chr15:75280477..75282648,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199580	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11072519	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12591994	0.85[ASN][1000 genomes]
rs12592477	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12593476	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593542	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594117	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289582	0.88[ASN][1000 genomes]
rs2304904	0.85[ASN][1000 genomes]
rs28394281	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3812943	0.89[ASN][1000 genomes]
rs3812946	0.86[ASN][1000 genomes]
rs3910748	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56828495	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56970592	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58068887	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58294763	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58403754	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58645417	0.84[ASN][1000 genomes]
rs59094290	0.89[ASN][1000 genomes]
rs61166993	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495135	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495136	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495137	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495138	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495140	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495142	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163390	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166105	0.84[AMR][1000 genomes]
rs7167415	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168638	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172715	0.92[ASN][1000 genomes]
rs7172989	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7173218	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174129	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179097	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181942	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182286	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7342591	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7342601	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73436579	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73436586	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73438537	0.81[ASN][1000 genomes]
rs73438554	0.84[AMR][1000 genomes]
rs74023908	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025863	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031545	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034149	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036573	0.89[ASN][1000 genomes]
rs8040961	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672926	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9672995	0.91[ASN][1000 genomes]
rs9672996	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9673012	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9788648	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55877218	SCAMP5	cis	Artery Tibial	GTEx
rs55877218	SCAMP5	cis	Esophagus Mucosa	GTEx
rs55877218	PPCDC	cis	Adipose Subcutaneous	GTEx
rs55877218	SCAMP5	cis	Thyroid	GTEx

Chromatin state (count:0 , 50 per page) page:

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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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