Variant report

Variant	rs6774725
Chromosome Location	chr3:160604849-160604850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap]
rs10433352	0.81[CEU][hapmap]
rs11711152	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713093	0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11916355	0.86[EUR][1000 genomes]
rs11922296	0.81[JPT][hapmap]
rs13071999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13073059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13256	0.90[CEU][hapmap]
rs13315565	0.94[CEU][hapmap]
rs1345156	1.00[CEU][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1348976	0.81[JPT][hapmap]
rs1374789	0.81[JPT][hapmap]
rs1374790	0.81[JPT][hapmap]
rs1447610	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1447615	0.81[JPT][hapmap]
rs1447622	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562464	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs16831563	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831796	0.81[CEU][hapmap]
rs1839016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839018	0.81[JPT][hapmap]
rs1868105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868108	0.82[GIH][hapmap]
rs1868109	0.81[JPT][hapmap]
rs2044571	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2197700	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2889390	0.85[JPT][hapmap]
rs35257491	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441337	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66872845	0.80[EUR][1000 genomes]
rs6768115	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801330	0.81[JPT][hapmap]
rs6801444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7624185	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs7628389	0.81[CEU][hapmap]
rs7641892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898677	0.81[CEU][hapmap]
rs935497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs956447	0.81[JPT][hapmap]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap]
rs9822435	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs9832109	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs9844267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9857482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9857855	0.84[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs9871801	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap]
rs9883566	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3391648	chr3:160602299-160620598	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6774725	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs6774725	B3GALNT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160604200-160605000	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr3:160604400-160605200	Enhancers	GM12878-XiMat	blood
3	chr3:160604400-160616600	Weak transcription	Psoas Muscle	Psoas
4	chr3:160604600-160606000	Weak transcription	Dnd41	blood

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