Variant report

Variant	rs12230675
Chromosome Location	chr12:42656546-42656547
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42631147..42633630-chr12:42655201..42657259,2	K562	blood:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000015153	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10492386	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10492387	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785332	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785336	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880257	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880263	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880274	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880276	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181347	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181348	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11181356	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181359	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181383	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181384	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181385	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181387	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11181388	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11181391	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181396	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11829883	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11831168	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11832197	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11834173	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227365	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228932	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12231307	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12579560	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12582652	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12582890	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17091018	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1988893	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2100546	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2198764	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382968	0.81[AFR][1000 genomes]
rs4586237	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60971233	0.91[ASN][1000 genomes]
rs61924344	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61940203	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61940227	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61940237	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7296847	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306744	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73114420	0.94[ASN][1000 genomes]
rs73116436	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314223	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7485381	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953509	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960726	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7965273	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978820	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs880161	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325211	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3397788	chr12:42636734-42665519	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12230675	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42654200-42660600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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