Variant report

Variant	rs10055468
Chromosome Location	chr5:114529748-114529749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10057172	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059320	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061960	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070542	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078804	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305130	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4041	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596375	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326953	0.84[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	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10055468	PGGT1B	cis	multi-tissue	Pritchard
rs10055468	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114522800-114543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
3	chr5:114525400-114531400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr5:114525800-114544800	Weak transcription	Primary T cells from cord blood	blood
5	chr5:114527600-114529800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:114527600-114530000	Weak transcription	Colonic Mucosa	Colon
7	chr5:114528000-114563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:114529200-114562600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:114529400-114531400	Enhancers	Stomach Mucosa	stomach
10	chr5:114529400-114532000	Enhancers	Duodenum Mucosa	Duodenum
11	chr5:114529600-114530400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr5:114529600-114531400	Enhancers	Liver	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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