Variant report

Variant	rs1562464
Chromosome Location	chr3:160681614-160681615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160680508..160683340-chr3:160683641..160685438,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap];0.80[AMR][1000 genomes]
rs10433352	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs11711152	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs11713093	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11715733	0.82[AMR][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs11718966	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs11720263	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs11916355	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12696112	0.85[EUR][1000 genomes]
rs12696113	0.84[EUR][1000 genomes]
rs13060718	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13071999	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13073059	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13085336	0.90[CEU][hapmap]
rs13098896	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13256	0.90[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs13315565	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1345156	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1374795	0.81[JPT][hapmap]
rs1447610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs1447622	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs16831796	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs1868105	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1868107	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs1868109	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2014810	0.82[AMR][1000 genomes]
rs2044571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2889390	0.90[JPT][hapmap]
rs4521287	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs4679920	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs6441338	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs66872845	0.80[EUR][1000 genomes]
rs6768115	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs6774725	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs6801444	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6806015	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73021215	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7610432	0.82[AMR][1000 genomes]
rs7624185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7628389	0.81[CEU][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs7641892	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs898677	0.81[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs935497	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs956447	0.85[JPT][hapmap]
rs964533	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9812507	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9822435	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9832109	1.00[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9844267	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs9845943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs9857482	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9857855	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs9860537	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9862086	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9871801	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9880269	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9883566	0.90[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	esv3462791	chr3:160680085-160686174	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3462792	chr3:160680137-160686148	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3462790	chr3:160680198-160686110	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3462793	chr3:160680198-160686110	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv16422	chr3:160680271-160685991	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv592129	chr3:160681614-160684597	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv517658	chr3:160681614-160684720	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv592130	chr3:160681614-160685894	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1562464	B3GALNT1	cis	lymphoblastoid	seeQTL
rs1562464	SPTSSB	cis	Thyroid	GTEx
rs1562464	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160667400-160696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:160670200-160686600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:160670400-160686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:160670600-160682200	Weak transcription	Left Ventricle	heart
6	chr3:160678400-160697600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:160679000-160686600	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:160680000-160683600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:160680000-160684400	Weak transcription	Dnd41	blood
10	chr3:160681000-160686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:160681600-160684800	Weak transcription	Primary hematopoietic stem cells	blood

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