Variant report

Variant	rs9474647
Chromosome Location	chr6:53618520-53618521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11759427	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11759473	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12662433	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3813850	0.92[TSI][hapmap]
rs4478409	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4486000	0.81[TSI][hapmap]
rs4712042	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57853292	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62399937	0.82[ASN][1000 genomes]
rs62399939	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7759593	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463970	1.00[CEU][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9463971	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463975	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463976	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9474643	1.00[CEU][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474650	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9474647	C6orf142	cis	cerebellum	SCAN
rs9474647	RAB23	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53606400-53619600	Weak transcription	Right Atrium	heart
3	chr6:53614800-53618800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:53616200-53618800	Enhancers	HMEC	breast
5	chr6:53616600-53619400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:53616800-53619000	Enhancers	Hela-S3	cervix
7	chr6:53617200-53618600	Enhancers	HUVEC	blood vessel
8	chr6:53617400-53618600	Enhancers	Placenta	Placenta
9	chr6:53617400-53618600	Enhancers	HSMM	muscle
10	chr6:53617800-53618800	Enhancers	NHEK	skin
11	chr6:53617800-53619000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:53618200-53630200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:53618400-53618800	Enhancers	Esophagus	oesophagus

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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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