Variant report

Variant	rs899275
Chromosome Location	chr3:161042104-161042105
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160987740..160990491-chr3:161040751..161042747,3	MCF-7	breast:
2	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
3	chr3:161040142..161042354-chr3:161082440..161084651,2	MCF-7	breast:
4	chr3:160942925..160944989-chr3:161039772..161043116,3	MCF-7	breast:
5	chr3:161024510..161027943-chr3:161039749..161042505,4	MCF-7	breast:
6	chr3:160940058..160942666-chr3:161042036..161044035,3	MCF-7	breast:
7	chr3:161009978..161012586-chr3:161040587..161043038,3	MCF-7	breast:
8	chr3:161040559..161042979-chr3:161133154..161135842,2	MCF-7	breast:
9	chr3:161040460..161042970-chr3:161125296..161126963,2	MCF-7	breast:
10	chr3:161040220..161042157-chr3:161138208..161140268,2	MCF-7	breast:
11	chr3:161006869..161011120-chr3:161039575..161043501,7	MCF-7	breast:
12	chr3:161041936..161043684-chr3:161128783..161133001,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10804790	0.81[EUR][1000 genomes]
rs10936223	0.84[AMR][1000 genomes]
rs10936224	0.87[AMR][1000 genomes]
rs1154701	0.86[EUR][1000 genomes]
rs12486253	0.95[EUR][1000 genomes]
rs12495310	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631850	0.84[AMR][1000 genomes]
rs13083229	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1382427	0.81[EUR][1000 genomes]
rs1382428	0.80[EUR][1000 genomes]
rs1478568	0.95[EUR][1000 genomes]
rs1600209	0.81[EUR][1000 genomes]
rs1993891	0.81[EUR][1000 genomes]
rs336541	0.81[EUR][1000 genomes]
rs336543	0.81[EUR][1000 genomes]
rs336548	0.81[EUR][1000 genomes]
rs336568	0.82[EUR][1000 genomes]
rs336572	0.83[EUR][1000 genomes]
rs336580	0.82[EUR][1000 genomes]
rs336582	0.82[EUR][1000 genomes]
rs4290817	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470535	0.94[EUR][1000 genomes]
rs4518145	0.83[EUR][1000 genomes]
rs4560315	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4856714	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4856738	0.94[EUR][1000 genomes]
rs4856739	0.85[EUR][1000 genomes]
rs4856767	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4856768	0.95[EUR][1000 genomes]
rs55688744	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6441370	0.86[EUR][1000 genomes]
rs6441371	0.84[EUR][1000 genomes]
rs6768818	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774276	0.82[EUR][1000 genomes]
rs6789388	0.85[EUR][1000 genomes]
rs6791213	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809256	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611367	0.86[EUR][1000 genomes]
rs7613227	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7613358	0.92[EUR][1000 genomes]
rs7627528	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632797	0.86[EUR][1000 genomes]
rs7633186	0.86[EUR][1000 genomes]
rs7636941	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7638668	0.81[EUR][1000 genomes]
rs7652267	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809522	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9815222	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834659	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839527	0.95[EUR][1000 genomes]
rs9864752	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9872514	0.80[EUR][1000 genomes]
rs9879687	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs899275	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161041400-161042400	Enhancers	Stomach Mucosa	stomach
2	chr3:161042000-161042200	Flanking Active TSS	HepG2	liver

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