Variant report

Variant	rs2909817
Chromosome Location	chr5:116068926-116068927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1027292	0.96[MEX][hapmap];0.85[TSI][hapmap]
rs1565701	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2909816	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909818	0.87[ASN][1000 genomes]
rs2909825	0.82[EUR][1000 genomes]
rs2933594	0.83[ASN][1000 genomes]
rs2933595	0.83[ASN][1000 genomes]
rs2933596	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2933597	0.85[ASN][1000 genomes]
rs2933628	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs2933630	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs2964686	0.83[ASN][1000 genomes]
rs2964687	0.83[ASN][1000 genomes]
rs2964688	0.83[ASN][1000 genomes]
rs2964689	0.84[ASN][1000 genomes]
rs2964690	0.86[ASN][1000 genomes]
rs2964691	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964694	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs878401	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763490	chr5:115918339-116138525	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv830456	chr5:115969066-116170718	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv527974	chr5:115987168-116303678	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv462403	chr5:115994775-116284378	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv599485	chr5:115994775-116284378	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1030056	chr5:116008971-116278725	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1033140	chr5:116035131-116314673	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2909817	CCDC112	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116062600-116069200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:116063600-116069600	Weak transcription	Right Ventricle	heart
3	chr5:116065600-116069800	Weak transcription	Left Ventricle	heart
4	chr5:116067600-116069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:116068000-116069000	Weak transcription	Fetal Lung	lung
6	chr5:116068000-116069800	Weak transcription	Placenta	Placenta
7	chr5:116068000-116070000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:116068000-116071000	Enhancers	Colon Smooth Muscle	Colon
9	chr5:116068200-116069400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:116068200-116069400	Weak transcription	Fetal Heart	heart
11	chr5:116068200-116069600	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:116068200-116070600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:116068400-116069000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:116068400-116076600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:116068800-116071200	Enhancers	Rectal Smooth Muscle	rectum

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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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