Variant report

Variant	rs28576277
Chromosome Location	chr6:74164544-74164545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:74163979-74164792	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:74164005-74164876	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr6:74164485-74164854	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:74163979-74164807	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr6:74164387-74164859	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr6:74164002-74164885	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr6:74164416-74164839	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr6:74163980-74164806	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:74163983-74164794	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr6:74163983-74164835	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74160479..74164788-chr6:74167921..74174562,8	MCF-7	breast:
2	chr6:74160381..74163624-chr6:74164100..74167084,3	MCF-7	breast:
3	chr6:74164443..74166634-chr6:74168555..74172603,3	MCF-7	breast:
4	chr6:74160478..74163354-chr6:74163726..74166280,3	MCF-7	breast:
5	chr6:74164533..74167289-chr6:74290489..74292657,2	MCF-7	breast:
6	chr6:74164299..74168404-chr6:74171305..74174933,6	K562	blood:
7	6:74000304-74012200..6:74160392-74184826	K562	blood:
8	chr6:74163964..74167099-chr6:74229321..74231393,3	MCF-7	breast:
9	chr6:74163748..74166075-chr6:74168317..74170786,2	K562	blood:
10	chr6:74164240..74168881-chr6:74169286..74175928,7	K562	blood:

No data

Variant related genes	Relation type
MB21D1	TF binding region
ENSG00000135297	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000234882	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12198468	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1245345	0.81[ASN][1000 genomes]
rs1390080	0.81[ASN][1000 genomes]
rs1713862	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4708060	0.81[ASN][1000 genomes]
rs516203	0.81[ASN][1000 genomes]
rs523883	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs535902	0.81[ASN][1000 genomes]
rs541178	0.81[ASN][1000 genomes]
rs608026	0.81[ASN][1000 genomes]
rs658475	0.81[ASN][1000 genomes]
rs674708	0.81[ASN][1000 genomes]
rs679272	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6907936	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7749897	0.81[ASN][1000 genomes]
rs9293930	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9341424	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9352000	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9352002	0.81[ASN][1000 genomes]
rs9352007	0.81[ASN][1000 genomes]
rs9360689	0.81[ASN][1000 genomes]
rs9446904	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs951332	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv830693	chr6:74049342-74216080	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
4	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28576277	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74162200-74170800	Weak transcription	Liver	Liver
2	chr6:74162200-74170800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:74162200-74170800	Weak transcription	Lung	lung
4	chr6:74162400-74164600	Weak transcription	Right Ventricle	heart
5	chr6:74162400-74165200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:74162400-74165600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:74162400-74165800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:74162400-74165800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:74162400-74169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:74162400-74170800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:74162400-74170800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:74162400-74170800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:74162600-74165400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:74162600-74165600	Weak transcription	GM12878-XiMat	blood
15	chr6:74162600-74169200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:74162600-74169200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:74162600-74170800	Weak transcription	Osteobl	bone
18	chr6:74162800-74169800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:74163000-74165600	Weak transcription	Hela-S3	cervix
20	chr6:74163200-74164600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:74163200-74165600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:74163200-74169400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:74163800-74166200	Enhancers	Primary B cells from cord blood	blood
24	chr6:74164200-74164600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:74164200-74164800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:74164200-74164800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr6:74164200-74164800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:74164200-74164800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:74164200-74164800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:74164200-74164800	Enhancers	HMEC	breast
31	chr6:74164200-74165000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:74164200-74166200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:74164200-74166400	Enhancers	NHEK	skin
34	chr6:74164400-74165600	Weak transcription	K562	blood
35	chr6:74164400-74170800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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