Variant report

Variant	rs11180989
Chromosome Location	chr12:41935609-41935610
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10219633	0.81[JPT][hapmap]
rs10459287	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10506193	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10506194	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10785269	0.82[CEU][hapmap]
rs10880068	0.81[JPT][hapmap]
rs10880069	0.81[JPT][hapmap]
rs10880070	0.81[JPT][hapmap]
rs10880081	0.89[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880082	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880084	1.00[JPT][hapmap]
rs10880085	0.81[JPT][hapmap]
rs10880086	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880087	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880088	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880089	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880090	1.00[JPT][hapmap]
rs10880091	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880093	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880095	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880096	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880097	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880101	0.90[JPT][hapmap]
rs10880102	0.91[JPT][hapmap]
rs11180840	0.81[JPT][hapmap]
rs11180844	0.81[JPT][hapmap]
rs11180845	0.81[JPT][hapmap]
rs11180860	0.81[JPT][hapmap]
rs11180873	0.81[JPT][hapmap]
rs11180875	0.81[JPT][hapmap]
rs11180879	0.81[JPT][hapmap]
rs11180883	0.81[JPT][hapmap]
rs11180886	0.81[JPT][hapmap]
rs11180903	0.81[JPT][hapmap]
rs11180913	0.81[JPT][hapmap]
rs11180917	0.81[JPT][hapmap]
rs11180921	0.81[JPT][hapmap]
rs11180922	0.81[JPT][hapmap]
rs11180928	0.81[JPT][hapmap]
rs11180932	0.81[JPT][hapmap]
rs11180936	0.84[CEU][hapmap]
rs11180941	0.81[JPT][hapmap]
rs11180943	0.88[CEU][hapmap]
rs11180944	0.81[JPT][hapmap]
rs11180947	0.81[JPT][hapmap]
rs11180948	0.81[JPT][hapmap]
rs11180949	0.81[JPT][hapmap]
rs11180950	0.86[JPT][hapmap]
rs11180952	0.81[JPT][hapmap]
rs11180954	0.81[JPT][hapmap]
rs11180955	0.81[JPT][hapmap]
rs11180959	0.81[JPT][hapmap]
rs11180961	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11180962	0.81[JPT][hapmap]
rs11180963	0.81[JPT][hapmap]
rs11180964	0.81[JPT][hapmap]
rs11180965	0.81[JPT][hapmap]
rs11180968	0.81[JPT][hapmap]
rs11180969	0.81[JPT][hapmap]
rs11180970	1.00[JPT][hapmap]
rs11180972	1.00[JPT][hapmap]
rs11180973	1.00[JPT][hapmap]
rs11180974	1.00[JPT][hapmap]
rs11180975	1.00[JPT][hapmap]
rs11180976	1.00[JPT][hapmap]
rs11180978	1.00[JPT][hapmap]
rs11180979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180982	0.82[ASN][1000 genomes]
rs11180983	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11180984	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180988	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180994	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11180995	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11180997	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11181000	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11181005	0.91[JPT][hapmap]
rs11181010	0.90[JPT][hapmap]
rs12227303	0.91[JPT][hapmap]
rs12227540	1.00[JPT][hapmap]
rs12229610	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12230775	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12231433	0.81[JPT][hapmap]
rs12232019	0.81[JPT][hapmap]
rs12372586	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12581707	0.90[JPT][hapmap]
rs12582909	0.91[JPT][hapmap]
rs12582987	0.81[JPT][hapmap]
rs1379766	0.81[JPT][hapmap]
rs1458153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458172	1.00[JPT][hapmap]
rs1458173	1.00[JPT][hapmap]
rs17129436	0.89[JPT][hapmap]
rs17129470	0.91[JPT][hapmap]
rs17579291	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17835484	1.00[JPT][hapmap]
rs1902908	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2054211	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2125289	1.00[JPT][hapmap]
rs2608709	0.84[CEU][hapmap]
rs285569	1.00[ASW][hapmap]
rs285578	0.91[JPT][hapmap]
rs285583	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs285586	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs285587	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3110189	0.84[CEU][hapmap]
rs3214027	0.81[JPT][hapmap]
rs4768355	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs725527	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73130674	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7968280	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11180989	PDZRN4	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41925600-41949800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:41925800-41944800	Weak transcription	Brain Germinal Matrix	brain

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