Variant report

Variant	rs13315565
Chromosome Location	chr3:160754626-160754627
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160749654..160751759-chr3:160753566..160755069,2	MCF-7	breast:
2	chr3:160745725..160748261-chr3:160752866..160755134,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10154889	0.88[CEU][hapmap];0.89[AMR][1000 genomes]
rs10433352	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11711152	0.94[CEU][hapmap]
rs11715733	0.90[AMR][1000 genomes]
rs11717272	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11718966	0.94[CEU][hapmap]
rs11720263	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11915989	0.83[EUR][1000 genomes]
rs11922957	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11922959	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12696112	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12696113	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13060601	0.86[EUR][1000 genomes]
rs13060718	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13062651	0.88[AMR][1000 genomes]
rs13071892	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13071999	0.94[CEU][hapmap]
rs13073059	0.94[CEU][hapmap]
rs13085336	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs13098896	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13256	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1345156	0.94[CEU][hapmap]
rs1447610	0.94[CEU][hapmap]
rs1447622	1.00[CEU][hapmap]
rs1562464	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1599388	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16831796	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16831886	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1868105	0.94[CEU][hapmap]
rs1868107	0.94[CEU][hapmap]
rs2014810	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2044571	0.94[CEU][hapmap]
rs34221255	0.83[AMR][1000 genomes]
rs34630898	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35914913	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4494975	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4521287	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4679920	0.94[CEU][hapmap]
rs4679929	0.87[AMR][1000 genomes]
rs4856700	0.82[CEU][hapmap]
rs57145341	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6441338	1.00[CEU][hapmap]
rs6441362	0.86[EUR][1000 genomes]
rs6768115	0.94[CEU][hapmap]
rs6772723	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6774725	0.94[CEU][hapmap]
rs6794882	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6801444	0.94[CEU][hapmap]
rs6806015	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68166680	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73021215	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73023235	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7433918	0.80[AMR][1000 genomes]
rs7610432	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7618924	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7624185	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7628389	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7641892	0.94[CEU][hapmap]
rs898677	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs935497	0.94[CEU][hapmap]
rs964533	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9812507	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9822435	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9832109	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9844267	0.94[CEU][hapmap]
rs9845943	0.94[CEU][hapmap]
rs9857482	0.94[CEU][hapmap]
rs9857855	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9860537	0.94[CEU][hapmap]
rs9862086	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876142	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9880269	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883566	0.94[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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	nsv979791	chr3:160753362-160754754	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13315565	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs13315565	SPTSSB	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160749800-160759000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:160752200-160755200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:160752200-160755200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:160753000-160755000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:160753800-160755000	Enhancers	Primary B cells from cord blood	blood
7	chr3:160753800-160755200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:160753800-160763200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:160754000-160755000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:160754000-160755200	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:160754000-160755200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:160754200-160755200	Enhancers	HUVEC	blood vessel
13	chr3:160754200-160760000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160754400-160756200	Weak transcription	Osteobl	bone
15	chr3:160754400-160756600	Weak transcription	NH-A	brain

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