Variant report

Variant	rs7730020
Chromosome Location	chr5:40657952-40657953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11739531	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2221490	0.80[AMR][1000 genomes]
rs2888173	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4133101	0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs4314453	0.85[EUR][1000 genomes]
rs4412150	0.83[EUR][1000 genomes]
rs4434423	0.84[CEU][hapmap]
rs4546432	0.87[CEU][hapmap]
rs4607392	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6451533	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7716982	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9687297	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7730020	MGC42105	cis	cerebellum	SCAN
rs7730020	PLA2G4C	trans	lymphoblastoid	seeQTL
rs7730020	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs7730020	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40655600-40660600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr5:40655600-40660600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr5:40655600-40669600	Weak transcription	Thymus	Thymus
4	chr5:40656200-40658200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:40656200-40658200	Weak transcription	Dnd41	blood
6	chr5:40656200-40658600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:40656400-40658400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:40656400-40658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:40657000-40658000	Weak transcription	Primary T cells from cord blood	blood

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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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