Variant report

Variant	rs9832109
Chromosome Location	chr3:160723364-160723365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10433352	0.85[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10513560	0.83[CHD][hapmap]
rs11711152	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs11713093	0.86[EUR][1000 genomes]
rs11713987	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11715733	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap]
rs11720263	0.90[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11916355	0.82[EUR][1000 genomes]
rs11922957	0.89[AMR][1000 genomes]
rs11922959	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12690576	0.86[GIH][hapmap]
rs12696112	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12696113	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13060718	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13062651	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13071892	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13071999	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs13073059	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13085336	0.90[CEU][hapmap]
rs13098896	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13256	0.90[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1345156	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1374787	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs1374790	0.84[JPT][hapmap]
rs1374795	0.85[JPT][hapmap]
rs1447610	1.00[CEU][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs1447622	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs1530636	0.83[CHD][hapmap]
rs1562464	1.00[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1599388	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16831886	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1868105	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1868107	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs1868109	0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs2014810	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2044571	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2376476	0.95[ASN][1000 genomes]
rs2376477	0.97[ASN][1000 genomes]
rs2889390	0.86[JPT][hapmap]
rs34221255	0.81[AMR][1000 genomes]
rs34630898	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35914913	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4494975	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4521287	0.90[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes]
rs4679920	1.00[CEU][hapmap]
rs4679928	0.97[ASN][1000 genomes]
rs4679929	0.90[AMR][1000 genomes]
rs57145341	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap]
rs6441345	0.80[CHD][hapmap]
rs6768115	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs6772723	0.90[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs6774203	0.80[CHD][hapmap]
rs6774725	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs6794882	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6801444	1.00[CEU][hapmap]
rs6806015	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68166680	0.89[AMR][1000 genomes]
rs73021215	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73023235	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs733948	0.86[GIH][hapmap]
rs7433918	0.82[AMR][1000 genomes]
rs7610432	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7611005	0.96[ASN][1000 genomes]
rs7618455	0.81[AMR][1000 genomes]
rs7618924	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7624185	1.00[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7628389	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7641892	1.00[CEU][hapmap]
rs898677	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs935497	1.00[CEU][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs956447	0.90[JPT][hapmap]
rs964533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822435	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9844267	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs9845943	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs9857482	1.00[CEU][hapmap]
rs9857855	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9858335	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs9860537	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs9862086	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9871801	0.81[EUR][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9880269	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9883566	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv518915	chr3:160723364-160724933	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9832109	B3GALNT1	cis	lymphoblastoid	seeQTL
rs9832109	C3orf57	cis	parietal	SCAN
rs9832109	SPTSSB	cis	Thyroid	GTEx
rs9832109	PPM1L	cis	cerebellum	SCAN
rs9832109	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160721400-160724800	Weak transcription	Brain Anterior Caudate	brain

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