Variant report

Variant	rs10880222
Chromosome Location	chr12:42411344-42411345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10492386	0.93[JPT][hapmap]
rs10492387	0.85[JPT][hapmap]
rs10785332	0.80[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs10880263	0.93[JPT][hapmap]
rs11181281	0.83[EUR][1000 genomes]
rs11181282	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11181283	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11181317	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11181332	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs11181344	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs11181347	0.80[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs11181356	0.80[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs11181359	0.80[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs12231330	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579560	0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs17090898	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17091018	0.80[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs17494245	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3852593	0.82[JPT][hapmap];0.90[MEX][hapmap]
rs3852594	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap]
rs3864939	0.86[AMR][1000 genomes]
rs56085053	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61942479	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7965273	0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap]
rs7972986	0.90[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][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	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
rs10880222	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs10880222	ZCRB1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42402800-42417000	Weak transcription	Right Atrium	heart
2	chr12:42409200-42416400	Weak transcription	Brain Germinal Matrix	brain
3	chr12:42409200-42417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:42409600-42415000	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:42410800-42411400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:42410800-42411400	Enhancers	GM12878-XiMat	blood
7	chr12:42410800-42411600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:42411000-42411400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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