Variant report

Variant	rs4856767
Chromosome Location	chr3:161004379-161004380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160995837..160997723-chr3:161002704..161004824,2	MCF-7	breast:
2	chr3:161002232..161004388-chr3:161087385..161090642,3	MCF-7	breast:
3	chr3:161000404..161005732-chr3:161006848..161011862,5	MCF-7	breast:
4	chr3:161002241..161004696-chr3:161089153..161092040,2	MCF-7	breast:
5	chr3:160990275..160995115-chr3:161003197..161013240,19	MCF-7	breast:
6	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
7	chr3:161001819..161012846-chr3:161052557..161065154,32	MCF-7	breast:
8	chr3:161003732..161004666-chr6:94043528..94044524,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10936223	0.86[AMR][1000 genomes]
rs10936224	0.89[AMR][1000 genomes]
rs1154701	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12486253	0.99[EUR][1000 genomes]
rs12495310	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631850	0.86[AMR][1000 genomes]
rs13083229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382427	0.82[CEU][hapmap]
rs1478565	0.82[CEU][hapmap]
rs1478568	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs163328	0.83[CEU][hapmap]
rs189270	0.82[CEU][hapmap]
rs1993891	0.82[CEU][hapmap]
rs336541	0.83[CEU][hapmap]
rs336543	0.82[CEU][hapmap]
rs336567	0.83[CEU][hapmap]
rs336570	0.82[CEU][hapmap]
rs336572	0.85[CEU][hapmap]
rs336577	0.83[CEU][hapmap]
rs336580	0.96[CEU][hapmap]
rs336583	0.82[CEU][hapmap]
rs336585	0.82[CEU][hapmap]
rs336586	0.86[CEU][hapmap]
rs336589	0.89[CEU][hapmap]
rs336590	0.89[CEU][hapmap]
rs336591	0.89[CEU][hapmap]
rs336593	0.86[CEU][hapmap]
rs339101	0.82[CEU][hapmap]
rs3849524	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4273380	0.83[CEU][hapmap]
rs4290817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4370045	0.82[CEU][hapmap]
rs4470535	0.99[EUR][1000 genomes]
rs4493449	0.83[CEU][hapmap]
rs4518145	0.86[EUR][1000 genomes]
rs4560315	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs456611	0.82[CEU][hapmap]
rs4597724	0.82[CEU][hapmap]
rs460508	0.82[CEU][hapmap]
rs4618258	0.81[AMR][1000 genomes]
rs462514	0.96[CEU][hapmap]
rs463928	0.82[CEU][hapmap]
rs464766	0.83[CEU][hapmap]
rs4856714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856738	0.99[EUR][1000 genomes]
rs4856739	0.89[EUR][1000 genomes]
rs4856768	1.00[EUR][1000 genomes]
rs55688744	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441370	0.90[EUR][1000 genomes]
rs6441371	0.88[EUR][1000 genomes]
rs6441373	0.83[CEU][hapmap]
rs6765269	0.82[CEU][hapmap]
rs6768818	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6774276	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6775627	0.81[CEU][hapmap]
rs6789388	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6791213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794601	0.82[CEU][hapmap]
rs6809256	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611367	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7613227	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7613358	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7615592	0.83[CEU][hapmap]
rs7623206	0.83[CEU][hapmap]
rs7627528	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7632797	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7633186	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7636941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647327	0.81[EUR][1000 genomes]
rs7652267	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];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7653233	0.81[EUR][1000 genomes]
rs7653361	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs899275	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9790314	0.81[EUR][1000 genomes]
rs9809522	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821201	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9834659	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839527	1.00[EUR][1000 genomes]
rs9850455	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9864752	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9870059	0.81[EUR][1000 genomes]
rs9872514	0.83[CEU][hapmap]
rs9879687	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4856767	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
2	chr3:161003400-161008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:161003400-161009200	Weak transcription	NHEK	skin
4	chr3:161003600-161008000	Weak transcription	Esophagus	oesophagus
5	chr3:161003600-161009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:161003600-161009000	Weak transcription	HMEC	breast
7	chr3:161004000-161007200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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