Variant report

Variant	rs10880230
Chromosome Location	chr12:42450253-42450254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42446010..42448026-chr12:42450147..42452999,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10459290	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs10492388	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1059360	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10785333	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10785334	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10880220	0.81[AMR][1000 genomes]
rs10880259	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10880260	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs10880261	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10880264	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10880268	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10880269	0.83[JPT][hapmap]
rs11181289	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11181308	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11181364	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs12371615	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12372597	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7312933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs7957213	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969415	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974654	0.87[CHB][hapmap];0.86[JPT][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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv832387	chr12:42345541-42465505	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10880230	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs10880230	GXYLT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42449200-42450800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:42449600-42450800	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:42449800-42450600	Enhancers	Primary B cells from cord blood	blood
4	chr12:42449800-42450600	Enhancers	GM12878-XiMat	blood
5	chr12:42449800-42450600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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