Variant report

Variant	rs17099254
Chromosome Location	chr12:63692495-63692496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1250678	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1251629	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1266060	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1520722	0.92[ASN][1000 genomes]
rs17099264	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61934689	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61934690	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61934691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61934692	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61934693	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61934696	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61934697	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73318047	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs786852	0.92[ASN][1000 genomes]
rs7969845	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs813093	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv1035736	chr12:63526274-63920372	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541510	chr12:63526274-63920372	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1052866	chr12:63562442-63879794	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv541511	chr12:63562442-63879794	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv832438	chr12:63571652-63745827	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv832439	chr12:63688083-63865226	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv973949	chr12:63689599-63696178	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17099254	C12orf56	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63687600-63696000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:63688400-63695000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:63689200-63695000	Weak transcription	HMEC	breast
4	chr12:63691600-63692800	Enhancers	Fetal Kidney	kidney
5	chr12:63691800-63692600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:63692000-63692800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:63692200-63692600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:63692400-63692800	Enhancers	A549	lung

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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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