Variant report

Variant	rs12489992
Chromosome Location	chr3:179664925-179664926
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1474367	0.84[GIH][hapmap]
rs1524512	0.84[GIH][hapmap]
rs1524514	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34638709	1.00[ASN][1000 genomes]
rs73055495	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73057311	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73057355	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73057366	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060768	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290686	0.84[GIH][hapmap]
rs940523	0.81[MKK][hapmap]
rs9842358	1.00[JPT][hapmap]
rs9847354	0.90[ASN][1000 genomes]
rs9856937	0.84[GIH][hapmap]

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	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12489992	PSMD2	cis	cerebellum	SCAN
rs12489992	KCNMB2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179660400-179667600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:179660600-179666400	Weak transcription	Fetal Kidney	kidney
3	chr3:179660600-179666600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:179660600-179666800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:179660600-179667400	Weak transcription	Thymus	Thymus
6	chr3:179660600-179680800	Weak transcription	Pancreas	Pancrea
7	chr3:179661200-179666000	Weak transcription	Fetal Thymus	thymus
8	chr3:179661200-179667400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:179661200-179671400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:179661400-179666200	Weak transcription	Brain Anterior Caudate	brain
11	chr3:179664200-179667400	Weak transcription	Dnd41	blood
12	chr3:179664400-179666400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:179664800-179666000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:179664800-179666200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:179664800-179667200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:179664800-179667400	Weak transcription	Brain Angular Gyrus	brain

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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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