Variant report

Variant	rs1014855
Chromosome Location	chr3:157122142-157122143
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1074864	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10755111	0.85[JPT][hapmap]
rs10936077	0.81[JPT][hapmap]
rs10936088	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10936089	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392798	0.84[MEX][hapmap]
rs1403105	0.85[JPT][hapmap]
rs1456104	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456109	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2316712	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321743	0.85[JPT][hapmap]
rs3911402	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679790	0.85[JPT][hapmap]
rs4679791	0.85[JPT][hapmap]
rs4680353	0.85[JPT][hapmap]
rs722485	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9831686	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9837655	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9848774	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1014855	C3orf55	cis	parietal	SCAN
rs1014855	BRD7	cis	cerebellum	SCAN
rs1014855	PTX3	cis	cerebellum	SCAN
rs1014855	SSR3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
2	chr3:157107400-157128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:157107800-157123000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:157109400-157122800	Weak transcription	Osteobl	bone
5	chr3:157113400-157122600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:157113400-157129800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:157116000-157128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:157119000-157142800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:157120000-157142600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:157120200-157135800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:157120400-157123000	Weak transcription	NH-A	brain
12	chr3:157121600-157122200	Strong transcription	HUVEC	blood vessel

Quick Search:

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

what's new

Quick links