Variant report

Variant	rs12477212
Chromosome Location	chr2:231444383-231444384
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10167135	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804366	0.85[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10933341	0.85[ASN][1000 genomes]
rs10933345	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11674658	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12611446	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615477	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418016	0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs35028536	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6736679	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106818	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7562389	0.85[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9288669	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875953	chr2:231415189-231457819	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875955	chr2:231440555-231500805	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763113	chr2:231441828-231445303	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12477212	SPP2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231441000-231447200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:231442600-231445000	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:231443400-231451000	Weak transcription	Primary T cells from cord blood	blood
4	chr2:231443400-231453800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:231443400-231454400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:231443400-231454600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:231443600-231445800	Genic enhancers	GM12878-XiMat	blood
8	chr2:231443800-231447600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:231444000-231447400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:231444000-231447600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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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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