Variant report

Variant	rs2153263
Chromosome Location	chr1:165787435-165787436
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10800159	0.92[ASN][1000 genomes]
rs10918276	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12131697	0.85[ASN][1000 genomes]
rs12723198	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs14223	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1913846	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1999992	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2153264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790054	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2790056	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2790057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814470	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4474223	0.86[ASN][1000 genomes]
rs6426937	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs6426940	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6656194	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7411708	0.82[CHD][hapmap]
rs9427123	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv517792	chr1:165785503-165811729	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
4	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2153263	NUF2	cis	cerebellum	SCAN
rs2153263	ALDH9A1	cis	cerebellum	SCAN
rs2153263	ALDH9A1	cis	parietal	SCAN
rs2153263	F11R	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165785000-165787600	Enhancers	Fetal Heart	heart
2	chr1:165785400-165788000	Weak transcription	Gastric	stomach
3	chr1:165785600-165790600	Weak transcription	Right Atrium	heart
4	chr1:165786600-165787600	Enhancers	K562	blood
5	chr1:165787400-165787600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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