Variant report

Variant	rs2300697
Chromosome Location	chr2:31786637-31786638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10207755	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467911	0.80[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2208532	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268799	0.84[ASN][1000 genomes]
rs2300698	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300699	0.96[ASN][1000 genomes]
rs2300701	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2754530	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs413836	0.82[EUR][1000 genomes]
rs522638	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs523349	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs559555	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs632148	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6749019	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs676033	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs765138	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs806645	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1002988	chr2:31767131-31996924	Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2300697	FAM179A	cis	cerebellum	SCAN
rs2300697	SLC30A6	cis	cerebellum	SCAN
rs2300697	SLC30A6	cis	parietal	SCAN
rs2300697	IFT172	cis	parietal	SCAN
rs2300697	NLRC4	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31784400-31788200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:31784400-31788200	Weak transcription	HMEC	breast
3	chr2:31786000-31789400	Enhancers	Liver	Liver
4	chr2:31786400-31786800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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