Variant report

Variant	rs4516432
Chromosome Location	chr2:116381897-116381898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10205583	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205952	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13014914	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1448472	0.83[ASN][1000 genomes]
rs17044776	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35366253	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4849413	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7419743	0.87[ASN][1000 genomes]
rs7576503	0.83[ASN][1000 genomes]
rs7602082	0.84[ASN][1000 genomes]
rs7604938	0.83[ASN][1000 genomes]
rs950586	0.85[JPT][hapmap]
rs9711166	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1014859	chr2:116196951-116938584	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3323407	chr2:116374771-116402494	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4516432	GNAI2	trans	parietal	SCAN
rs4516432	SLC20A1	cis	parietal	SCAN
rs4516432	CHCHD5	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:116381000-116382000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:116381200-116382400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:116381200-116382600	Enhancers	Cortex derived primary cultured neurospheres	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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