Variant report

Variant	rs10875815
Chromosome Location	chr12:48834326-48834327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10875810	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705124	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2705125	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2731063	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2731092	0.80[CHB][hapmap]
rs2731096	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2731105	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4369449	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4542454	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4633503	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7139348	0.80[CHB][hapmap]
rs7309958	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7960406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10875815	SPATS2	cis	parietal	SCAN
rs10875815	RACGAP1	cis	cerebellum	SCAN
rs10875815	C12orf54	cis	multi-tissue	Pritchard
rs10875815	C12orf54	cis	lymphoblastoid	seeQTL
rs10875815	COL2A1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48833800-48840400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:48834200-48834600	Flanking Active TSS	Hela-S3	cervix
3	chr12:48834200-48840400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48834200-48840400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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