Variant report

Variant	rs4856768
Chromosome Location	chr3:161004392-161004393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1026572	0.82[AMR][1000 genomes]
rs1154701	0.90[EUR][1000 genomes]
rs12486253	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495310	0.99[EUR][1000 genomes]
rs13083229	0.99[EUR][1000 genomes]
rs1478568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1904204	0.80[ASN][1000 genomes]
rs336572	0.81[AMR][1000 genomes]
rs3849524	0.81[EUR][1000 genomes]
rs4290817	0.97[EUR][1000 genomes]
rs4470535	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4518145	0.86[EUR][1000 genomes]
rs4560315	0.99[EUR][1000 genomes]
rs4856714	0.98[EUR][1000 genomes]
rs4856738	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4856739	0.89[EUR][1000 genomes]
rs4856767	1.00[EUR][1000 genomes]
rs55688744	0.95[EUR][1000 genomes]
rs6441370	0.90[EUR][1000 genomes]
rs6441371	0.88[EUR][1000 genomes]
rs6768818	0.97[EUR][1000 genomes]
rs6774276	0.85[EUR][1000 genomes]
rs6789388	0.89[EUR][1000 genomes]
rs6791213	0.95[EUR][1000 genomes]
rs6809256	0.96[EUR][1000 genomes]
rs7611367	0.90[EUR][1000 genomes]
rs7613227	0.95[EUR][1000 genomes]
rs7613358	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7627528	0.99[EUR][1000 genomes]
rs7632797	0.90[EUR][1000 genomes]
rs7633186	0.89[EUR][1000 genomes]
rs7636941	0.98[EUR][1000 genomes]
rs7647327	0.81[EUR][1000 genomes]
rs7652267	0.98[EUR][1000 genomes]
rs7653233	0.81[EUR][1000 genomes]
rs7653361	0.81[EUR][1000 genomes]
rs899275	0.95[EUR][1000 genomes]
rs9290069	0.82[AMR][1000 genomes]
rs9790314	0.81[EUR][1000 genomes]
rs9809522	0.99[EUR][1000 genomes]
rs9815222	1.00[EUR][1000 genomes]
rs9821201	0.81[EUR][1000 genomes]
rs9834659	0.99[EUR][1000 genomes]
rs9839527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850455	0.81[EUR][1000 genomes]
rs9864752	0.88[EUR][1000 genomes]
rs9870059	0.81[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4856768	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs4856768	SPTSSB	cis	Heart Left Ventricle	GTEx

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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