Variant report

Variant	rs1316645
Chromosome Location	chr12:67328430-67328431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10506514	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs10506515	0.83[GIH][hapmap]
rs10878523	0.81[CEU][hapmap]
rs10878524	0.85[CEU][hapmap]
rs11176484	0.81[CEU][hapmap]
rs11176488	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12228305	0.81[CEU][hapmap]
rs12228327	0.81[AMR][1000 genomes]
rs12581024	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12811743	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12811914	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12812455	0.82[CEU][hapmap]
rs12813453	0.82[CEU][hapmap];0.80[GIH][hapmap]
rs1995503	0.81[CEU][hapmap]
rs1995504	0.81[CEU][hapmap]
rs7299111	0.85[EUR][1000 genomes]
rs7964701	0.81[ASN][1000 genomes]
rs962415	0.87[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053250	chr12:67067995-67381411	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1044939	chr12:67207260-67377982	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1036984	chr12:67273098-67427543	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1054433	chr12:67302689-67357930	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv541523	chr12:67302689-67357930	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1316645	C12orf66	cis	parietal	SCAN
rs1316645	XPOT	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67323800-67330400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:67327800-67328800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:67328200-67328800	Enhancers	Placenta	Placenta
4	chr12:67328200-67329200	Enhancers	Colon Smooth Muscle	Colon
5	chr12:67328400-67328800	Enhancers	HMEC	breast
6	chr12:67328400-67335200	Weak transcription	Rectal Smooth Muscle	rectum

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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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