Variant report

Variant	rs2427829
Chromosome Location	chr1:159282011-159282012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11265175	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12409540	1.00[YRI][hapmap]
rs17422585	0.82[ASW][hapmap]
rs2427830	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3845625	1.00[YRI][hapmap]
rs4548435	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6678381	0.95[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7511872	1.00[YRI][hapmap]
rs7522607	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7549785	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs7553515	1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv872487	chr1:159196765-159342439	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv872488	chr1:159218266-159336948	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv946449	chr1:159281974-159283532	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2427829	EFNA3	cis	cerebellum	SCAN
rs2427829	CD5L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159279200-159284400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:159279800-159284200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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