Variant report

Variant	rs9293930
Chromosome Location	chr6:74166098-74166099
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:74165531-74166201	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:74165631-74166217	Hela-S3	cervix:	n/a	chr6:74166147-74166158
3	STAT3	chr6:74165497-74166385	MCF10A-Er-Src	breast:	n/a	chr6:74166147-74166158
4	STAT3	chr6:74165504-74166364	MCF10A-Er-Src	breast:	n/a	chr6:74166147-74166158
5	FOS	chr6:74165510-74166349	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr6:74165573-74166329	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:74165526-74166379	MCF10A-Er-Src	breast:	n/a	chr6:74166147-74166158
8	TCF7L2	chr6:74165771-74166159	PANC-1	pancreas:	n/a	n/a
9	E2F4	chr6:74165630-74166130	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr6:74165592-74166338	Hela-S3	cervix:	n/a	chr6:74165785-74165796
11	MYC	chr6:74165654-74166143	NB4	blood:	n/a	n/a
12	FOS	chr6:74165498-74166329	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr6:74165474-74166118	K562	blood:	n/a	chr6:74165785-74165796
14	FOS	chr6:74165536-74166288	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr6:74165552-74166289	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr6:74165611-74166131	K562	blood:	n/a	chr6:74165785-74165796
17	STAT3	chr6:74165495-74166365	MCF10A-Er-Src	breast:	n/a	chr6:74166147-74166158
18	CEBPB	chr6:74165607-74166216	HepG2	liver:	n/a	chr6:74165785-74165796
19	STAT3	chr6:74165675-74166327	MCF10A-Er-Src	breast:	n/a	chr6:74166147-74166158
20	FOS	chr6:74165577-74166347	MCF10A-Er-Src	breast:	n/a	n/a
21	JUN	chr6:74165533-74166348	K562	blood:	n/a	chr6:74165782-74165795

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

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

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12198468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1245345	0.93[ASN][1000 genomes]
rs1390080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1713862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2643196	0.90[ASN][1000 genomes]
rs28576277	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs371827	0.89[JPT][hapmap]
rs4708060	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs479248	1.00[JPT][hapmap]
rs516203	0.93[ASN][1000 genomes]
rs523883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs535902	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs541178	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs606263	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs608026	0.93[ASN][1000 genomes]
rs621493	0.90[ASN][1000 genomes]
rs625478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs649909	0.84[ASN][1000 genomes]
rs654973	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs658475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs674708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs679272	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6907936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749897	0.93[ASN][1000 genomes]
rs780062	1.00[JPT][hapmap]
rs9341424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9352000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352002	0.93[ASN][1000 genomes]
rs9352007	0.93[ASN][1000 genomes]
rs9360689	0.93[ASN][1000 genomes]
rs9446904	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951332	0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9293930	MTO1	Cis_1M	lymphoblastoid	RTeQTL
rs9293930	CD109	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr6:74162400-74169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:74162400-74170800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:74162400-74170800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:74162400-74170800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:74162600-74169200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:74162600-74169200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:74162600-74170800	Weak transcription	Osteobl	bone
11	chr6:74162800-74169800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:74163200-74169400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:74163800-74166200	Enhancers	Primary B cells from cord blood	blood
14	chr6:74164200-74166200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:74164200-74166400	Enhancers	NHEK	skin
16	chr6:74164400-74170800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:74164800-74168000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:74164800-74170800	Weak transcription	HMEC	breast
19	chr6:74164800-74171200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:74165200-74166200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:74165400-74166400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:74165400-74166400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr6:74165400-74170800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:74165600-74166200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:74165600-74166200	Enhancers	K562	blood
26	chr6:74165600-74166400	Enhancers	Hela-S3	cervix
27	chr6:74165600-74166600	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:74165600-74166600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:74165600-74166800	Enhancers	HepG2	liver
30	chr6:74165800-74166200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:74165800-74166200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr6:74165800-74166200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:74166000-74169000	Weak transcription	GM12878-XiMat	blood

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