Variant report

Variant	rs12492016
Chromosome Location	chr3:118207924-118207925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28645420	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688115	0.86[AFR][1000 genomes]
rs56147469	0.82[AFR][1000 genomes]
rs7637943	0.93[ASN][1000 genomes]
rs9849379	0.93[ASN][1000 genomes]
rs9880522	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv460829	chr3:118195601-118229370	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591349	chr3:118195601-118229370	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv829690	chr3:118205361-118378010	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	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
rs12492016	PLA1A	cis	parietal	SCAN
rs12492016	SEC22A	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118206400-118208400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr3:118207000-118208200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:118207200-118208200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr3:118207200-118209400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:118207400-118208200	Enhancers	HMEC	breast
6	chr3:118207400-118208400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:118207600-118208000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:118207600-118208200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:118207600-118208400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:118207800-118208200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:118207800-118208200	Enhancers	Hela-S3	cervix
12	chr3:118207800-118208400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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

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