Variant report

Variant	rs658475
Chromosome Location	chr6:74195531-74195532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74193300..74196306-chr6:74229135..74232546,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12198468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245345	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1245346	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1245348	0.86[EUR][1000 genomes]
rs1390080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703461	1.00[CEU][hapmap]
rs1713862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1741886	1.00[CEU][hapmap]
rs2643196	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28576277	0.81[ASN][1000 genomes]
rs371827	0.89[JPT][hapmap]
rs4708060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708072	1.00[CEU][hapmap]
rs4708073	1.00[CEU][hapmap]
rs474661	1.00[CEU][hapmap]
rs479248	1.00[JPT][hapmap]
rs494841	1.00[CEU][hapmap]
rs506157	1.00[CEU][hapmap]
rs516203	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527606	1.00[CEU][hapmap]
rs535902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555840	1.00[CEU][hapmap]
rs570050	1.00[CEU][hapmap]
rs580531	1.00[CEU][hapmap]
rs583149	1.00[CEU][hapmap]
rs584078	0.82[CEU][hapmap]
rs584571	1.00[CEU][hapmap]
rs605857	0.81[ASN][1000 genomes]
rs606263	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs608026	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609790	1.00[CEU][hapmap]
rs609829	1.00[CEU][hapmap]
rs610260	1.00[CEU][hapmap]
rs611580	1.00[CEU][hapmap]
rs621493	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs625512	1.00[CEU][hapmap]
rs636605	1.00[CEU][hapmap]
rs649909	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs654973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs657212	1.00[CEU][hapmap]
rs671735	0.80[ASN][1000 genomes]
rs674708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678054	1.00[CEU][hapmap]
rs679272	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685491	1.00[CEU][hapmap]
rs686317	1.00[CEU][hapmap]
rs687210	1.00[CEU][hapmap]
rs6907936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7749897	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764560	1.00[CEU][hapmap]
rs7764983	1.00[CEU][hapmap]
rs780062	1.00[JPT][hapmap]
rs9293930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9293933	1.00[CEU][hapmap]
rs9341424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9352000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9352002	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352007	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360689	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446904	0.93[ASN][1000 genomes]
rs9446952	1.00[CEU][hapmap]
rs9446955	1.00[CEU][hapmap]
rs9446957	1.00[CEU][hapmap]
rs9446964	1.00[CEU][hapmap]
rs951332	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
7	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs658475	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74172200-74197200	Weak transcription	Fetal Heart	heart
2	chr6:74172200-74229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:74173400-74199000	Strong transcription	Fetal Thymus	thymus
4	chr6:74173600-74198800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:74173800-74198800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:74173800-74206200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:74175200-74198800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:74175200-74199200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr6:74175400-74199000	Strong transcription	Stomach Smooth Muscle	stomach
10	chr6:74175600-74198600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:74175600-74199000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:74175600-74199000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:74175800-74196800	Strong transcription	Liver	Liver
14	chr6:74175800-74197400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:74175800-74198000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:74175800-74198800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:74175800-74198800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:74175800-74198800	Strong transcription	Placenta	Placenta
19	chr6:74175800-74199000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:74175800-74199200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:74175800-74201000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:74176000-74198800	Strong transcription	Brain Anterior Caudate	brain
23	chr6:74176000-74198800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr6:74176000-74198800	Strong transcription	Fetal Intestine Large	intestine
25	chr6:74176000-74199000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:74176000-74199000	Strong transcription	Adipose Nuclei	Adipose
27	chr6:74176000-74199200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:74176600-74197400	Weak transcription	Fetal Brain Male	brain
29	chr6:74177600-74199000	Strong transcription	Dnd41	blood
30	chr6:74180600-74199000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:74181400-74199000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:74181600-74199000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:74181600-74199000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:74181800-74214800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:74182200-74196400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:74182200-74198800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:74182400-74198800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:74182400-74206200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:74182600-74198800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:74182600-74198800	Strong transcription	Fetal Intestine Small	intestine
41	chr6:74182600-74199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:74182800-74198800	Strong transcription	Primary T cells from cord blood	blood
43	chr6:74182800-74198800	Strong transcription	Fetal Stomach	stomach
44	chr6:74182800-74198800	Strong transcription	Lung	lung
45	chr6:74183000-74198800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:74183200-74198800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:74183800-74197400	Weak transcription	A549	lung
48	chr6:74183800-74198800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:74184000-74212000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:74185600-74196000	Strong transcription	Brain Cingulate Gyrus	brain

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