Variant report

Variant	rs9278036
Chromosome Location	chr6:33352360-33352361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33351561..33353215-chr6:33385874..33388766,2	MCF-7	breast:
2	chr6:33350087..33352952-chr6:33384695..33386243,2	K562	blood:
3	chr6:33245451..33247068-chr6:33352061..33354316,2	K562	blood:
4	chr6:33287030..33291405-chr6:33349040..33354148,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197283	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000112514	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1106606	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11751696	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11753355	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11756267	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11756767	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11757379	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs2235982	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41267647	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41271245	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4231	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55699469	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7752202	0.85[EUR][1000 genomes]
rs9277997	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9278001	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9278004	0.82[EUR][1000 genomes]
rs9278005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9278006	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9278007	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9278015	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9278016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9278019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9278027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9278028	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9278034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9278038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9278039	0.85[EUR][1000 genomes]
rs9278040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9278043	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9278044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9278045	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9278046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9278049	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9278036	B3GALT4	cis	multi-tissue	Pritchard
rs9278036	C6orf82	cis	multi-tissue	Pritchard
rs9278036	HLA-DRB5	cis	parietal	SCAN
rs9278036	PHF1	cis	multi-tissue	Pritchard
rs9278036	UHRF1BP1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33341000-33352400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33341200-33358600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:33343800-33359200	Weak transcription	Right Atrium	heart
4	chr6:33345600-33358800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:33348400-33358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:33348600-33352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:33350200-33352400	Weak transcription	K562	blood
8	chr6:33350200-33352600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:33351800-33352600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:33351800-33352600	Weak transcription	HepG2	liver
11	chr6:33351800-33358600	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:33352200-33352800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:33352200-33352800	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:33352200-33352800	Enhancers	Hela-S3	cervix

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