Variant report

Variant	rs580102
Chromosome Location	chr1:170068385-170068386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10800495	0.85[YRI][hapmap]
rs10919284	0.92[YRI][hapmap]
rs10919298	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10919299	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11803298	0.85[YRI][hapmap]
rs12123693	0.85[YRI][hapmap]
rs12124607	0.85[YRI][hapmap]
rs12126204	0.92[YRI][hapmap]
rs12137754	0.85[YRI][hapmap]
rs1360293	0.92[YRI][hapmap]
rs35688996	0.84[YRI][hapmap]
rs4656737	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4656738	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs518874	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs550297	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs575119	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs576152	0.80[CEU][hapmap]
rs6670191	0.92[YRI][hapmap]
rs7521273	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv999310	chr1:170065943-170223350	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs580102	BRP44	cis	parietal	SCAN
rs580102	KIFAP3	cis	parietal	SCAN
rs580102	SFT2D2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170068200-170068400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr1:170068200-170068600	Enhancers	HUES48 Cell Line	embryonic stem cell

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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

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