Variant report

Variant	rs6772723
Chromosome Location	chr3:160895074-160895075
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160894459..160896350-chr3:160939038..160940553,2	MCF-7	breast:
2	chr3:160892333..160895194-chr3:160896982..160899442,2	MCF-7	breast:
3	chr3:160817475..160820143-chr3:160893422..160895281,2	MCF-7	breast:
4	chr3:160815580..160817375-chr3:160895004..160897069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap]
rs10433352	0.81[MEX][hapmap]
rs10513564	0.88[CHD][hapmap];0.81[MEX][hapmap]
rs11711695	0.85[CHD][hapmap]
rs11712713	0.81[ASN][1000 genomes]
rs11717272	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11720263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11915989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922957	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11922959	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13059758	0.82[AMR][1000 genomes]
rs13060601	0.90[EUR][1000 genomes]
rs13071892	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13085336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098896	0.81[EUR][1000 genomes]
rs13256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1382429	0.90[CHD][hapmap];0.81[MEX][hapmap]
rs1450522	0.84[CHD][hapmap];0.81[MEX][hapmap]
rs1599388	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16831886	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2054710	0.84[CHD][hapmap]
rs28384382	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34105342	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34221255	0.80[ASN][1000 genomes]
rs34630898	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127376	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35589595	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35914913	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4494975	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4856703	0.91[CHD][hapmap];0.81[MEX][hapmap]
rs6441362	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441374	0.88[CHD][hapmap];0.81[MEX][hapmap]
rs6780536	0.88[CHD][hapmap];0.81[MEX][hapmap]
rs6794882	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68166680	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73023235	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7610800	0.84[YRI][hapmap]
rs7618924	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7624185	0.90[CEU][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs7628389	0.81[MEX][hapmap]
rs7638370	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898677	0.81[MEX][hapmap]
rs964533	0.90[CEU][hapmap]
rs9812507	0.90[CEU][hapmap]
rs9822435	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs9832109	0.90[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs9862086	0.83[EUR][1000 genomes]
rs9876142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9880269	0.83[EUR][1000 genomes]
rs9883566	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6772723	B3GALNT1	cis	lymphoblastoid	seeQTL
rs6772723	B3GALT3	cis	multi-tissue	Pritchard
rs6772723	SPTSSB	cis	Nerve Tibial	GTEx
rs6772723	SPTSSB	cis	Thyroid	GTEx
rs6772723	C3orf57	cis	parietal	SCAN
rs6772723	NMD3	cis	parietal	SCAN
rs6772723	PPM1L	cis	cerebellum	SCAN
rs6772723	SPTSSB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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