Variant report

Variant	rs285584
Chromosome Location	chr12:41946539-41946540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs169564	0.88[AMR][1000 genomes]
rs2599254	0.85[AMR][1000 genomes]
rs2730812	0.83[AMR][1000 genomes]
rs2730831	0.85[AMR][1000 genomes]
rs2730832	0.88[AMR][1000 genomes]
rs285551	0.88[AMR][1000 genomes]
rs285559	0.88[AMR][1000 genomes]
rs285588	0.91[MKK][hapmap];0.88[AMR][1000 genomes]
rs285591	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs285594	0.85[AMR][1000 genomes]
rs285596	0.85[AMR][1000 genomes]
rs285597	0.85[AMR][1000 genomes]
rs287087	0.91[MKK][hapmap];0.88[AMR][1000 genomes]
rs392217	0.85[AMR][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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs285584	PDZRN4	cis	brain	seeQTL
rs285584	PDZRN4	cis	parietal	SCAN
rs285584	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41925600-41949800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:41942800-41956800	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:41944600-41966200	Weak transcription	Ovary	ovary
4	chr12:41945400-41956800	Weak transcription	Aorta	Aorta
5	chr12:41945600-41947200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:41946400-41946800	Enhancers	HUVEC	blood vessel
7	chr12:41946400-41947000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr12:41946400-41947200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:41946400-41947200	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr12:41946400-41947200	Enhancers	Fetal Brain Male	brain
11	chr12:41946400-41947400	Enhancers	HUES64 Cell Line	embryonic stem cell

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