Variant report

Variant	rs2969775
Chromosome Location	chr2:47885476-47885477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1400633	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882450	0.82[ASN][1000 genomes]
rs2705766	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2705767	0.92[ASN][1000 genomes]
rs2944783	0.92[ASN][1000 genomes]
rs2969772	0.90[ASN][1000 genomes]
rs2969774	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv817599	chr2:47738456-47961099	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv457396	chr2:47866133-47956844	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv581771	chr2:47866133-47956844	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv581772	chr2:47874713-47892526	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Psychosis in Alzheimer's disease	22005930	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2969775	PLEKHH2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47880200-47885800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:47881800-47886200	Weak transcription	Right Atrium	heart
3	chr2:47882600-47886400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:47882800-47885800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:47882800-47887200	Enhancers	GM12878-XiMat	blood
6	chr2:47883000-47888800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:47883200-47888800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:47883200-47893000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:47883400-47888800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:47883600-47891200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:47884000-47887200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:47884000-47888800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:47885200-47887600	Enhancers	Primary B cells from peripheral blood	blood

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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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