Variant report

Variant	rs12796015
Chromosome Location	chr11:4944986-4944987
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	11:4940074-4947279..11:4988858-5002113	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000225003	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10500625	1.00[CEU][hapmap]
rs10500626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10500631	1.00[CEU][hapmap]
rs10836955	0.87[AMR][1000 genomes]
rs11034067	0.83[CEU][hapmap]
rs11034071	0.83[CEU][hapmap]
rs11034086	0.82[MKK][hapmap]
rs11034089	0.83[CEU][hapmap]
rs11034090	0.83[CEU][hapmap]
rs11034094	0.83[CEU][hapmap]
rs12785245	0.81[CEU][hapmap]
rs12785274	0.91[CEU][hapmap]
rs12786973	0.91[CEU][hapmap]
rs12787796	0.83[CEU][hapmap]
rs12788447	1.00[CEU][hapmap]
rs12793425	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12794894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs12795212	0.81[CEU][hapmap]
rs12796618	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs12799928	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12801368	0.91[CEU][hapmap]
rs12802922	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12804676	1.00[CEU][hapmap]
rs12806014	1.00[CEU][hapmap]
rs12806727	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1433899	1.00[CEU][hapmap]
rs1541946	0.83[CEU][hapmap]
rs17228176	0.83[CEU][hapmap]
rs17228183	0.83[CEU][hapmap]
rs17228218	0.83[CEU][hapmap]
rs17247598	0.85[CEU][hapmap]
rs17249369	0.91[CEU][hapmap]
rs17249695	0.83[CEU][hapmap]
rs17250199	0.91[CEU][hapmap]
rs17251220	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17251261	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17327845	0.91[CEU][hapmap]
rs17327907	0.91[CEU][hapmap]
rs17328143	0.83[CEU][hapmap]
rs17328337	0.83[CEU][hapmap]
rs17328371	0.82[MKK][hapmap]
rs17328565	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs17329242	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs17337601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17337649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1865282	0.83[CEU][hapmap]
rs2412395	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs34301246	0.84[EUR][1000 genomes]
rs34583466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34742470	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35408660	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35720831	0.85[EUR][1000 genomes]
rs35918613	0.84[EUR][1000 genomes]
rs4910686	0.91[CEU][hapmap]
rs4910687	0.83[CEU][hapmap]
rs4910688	0.82[CEU][hapmap]
rs7925039	0.82[EUR][1000 genomes]
rs7948040	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12796015	LSP1	cis	parietal	SCAN
rs12796015	OR56A5	cis	parietal	SCAN
rs12796015	FXC1	cis	cerebellum	SCAN
rs12796015	RPL27A	cis	cerebellum	SCAN
rs12796015	OR51E2	cis	parietal	SCAN
rs12796015	OR2D3	cis	parietal	SCAN
rs12796015	TSPAN32	cis	cerebellum	SCAN
rs12796015	OR52E8	cis	cerebellum	SCAN

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

No data

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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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