Variant report

Variant	rs6882769
Chromosome Location	chr5:40647763-40647764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10059002	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11739531	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2221490	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3792823	0.84[JPT][hapmap]
rs3792826	0.88[JPT][hapmap]
rs4133101	0.84[CEU][hapmap]
rs4266456	0.83[AFR][1000 genomes]
rs4434423	0.81[CEU][hapmap]
rs4546432	0.83[CEU][hapmap]
rs4607392	0.84[CEU][hapmap]
rs6451533	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7716982	0.81[AMR][1000 genomes];0.92[EUR][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	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6882769	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs6882769	PLA2G4C	trans	lymphoblastoid	seeQTL
rs6882769	SLC1A3	cis	cerebellum	SCAN
rs6882769	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs6882769	MGC42105	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40641800-40648400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:40644000-40654600	Weak transcription	Small Intestine	intestine
3	chr5:40645200-40648200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:40646400-40652400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:40646600-40652400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:40646800-40648000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:40647200-40652400	Weak transcription	Duodenum Mucosa	Duodenum

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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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