Variant report

Variant	rs1390080
Chromosome Location	chr6:74223153-74223154
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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74221323..74236726-chr6:74306065..74338770,101	K562	blood:
2	chr6:74221858..74225913-chr6:74344087..74347278,4	K562	blood:
3	chr14:96518133..96521112-chr6:74221890..74224860,2	K562	blood:
4	chr3:84968846..84970373-chr6:74221820..74224403,2	K562	blood:
5	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
6	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
7	6:74062967-74076046..6:74208016-74225478	GM12878	blood:
8	chr6:74213210..74215284-chr6:74222845..74225477,3	MCF-7	breast:
9	chr6:74221619..74224543-chr6:74299857..74301536,2	K562	blood:
10	chr15:42296173..42297692-chr6:74222948..74224753,3	K562	blood:
11	chr15:42297192..42298173-chr6:74222922..74223467,2	MCF-7	breast:
12	6:74078047-74099067..6:74208016-74225478	GM12878	blood:
13	chr6:74175829..74177746-chr6:74223041..74225034,2	K562	blood:
14	6:74160392-74184826..6:74208016-74225478	GM12878	blood:
15	chr6:74198950..74200761-chr6:74222278..74223851,2	MCF-7	breast:
16	chr6:74205300..74207492-chr6:74221549..74225584,4	K562	blood:
17	chr6:74222886..74227431-chr6:74328724..74331054,7	K562	blood:
18	chr6:74222835..74225633-chr6:74251462..74253727,3	K562	blood:
19	6:74099986-74112890..6:74208016-74225478	Hela-S3	cervix:
20	chr6:74205280..74208067-chr6:74222122..74224790,3	K562	blood:
21	chr6:74222972..74225246-chr6:74258116..74260995,4	K562	blood:
22	chr6:74222064..74227666-chr6:74315829..74323019,13	MCF-7	breast:
23	chr6:74223088..74226507-chr6:74303403..74307438,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224221	Chromatin interaction
ENSG00000218459	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000119899	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12198468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245345	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1245346	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1245348	0.88[EUR][1000 genomes]
rs1390082	0.84[YRI][hapmap]
rs1703461	1.00[CEU][hapmap]
rs1713862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1741886	1.00[CEU][hapmap]
rs2643196	0.88[AMR][1000 genomes];0.84[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];0.92[AMR][1000 genomes];0.96[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	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs523883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[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];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[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	0.83[AMR][1000 genomes];0.90[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	0.83[AMR][1000 genomes];0.90[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	0.90[ASN][1000 genomes]
rs654973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs657212	1.00[CEU][hapmap]
rs658475	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]
rs671735	0.80[ASN][1000 genomes]
rs674708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678054	1.00[CEU][hapmap]
rs679272	0.82[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	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[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];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9352000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9352002	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352007	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360689	0.90[AMR][1000 genomes];0.92[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	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv5350	chr6:74221995-74267088	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
10	nsv886159	chr6:74223153-74275405	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1390080	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74172200-74229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:74187600-74228400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:74192000-74225000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:74192200-74226000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:74192400-74225000	Weak transcription	Stomach Mucosa	stomach
6	chr6:74197800-74225200	Weak transcription	Colonic Mucosa	Colon
7	chr6:74198800-74225000	Weak transcription	Fetal Brain Male	brain
8	chr6:74199000-74224200	Weak transcription	A549	lung
9	chr6:74206000-74225000	Weak transcription	Pancreas	Pancrea
10	chr6:74208000-74225200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:74208400-74225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:74208400-74226000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:74208400-74226400	Weak transcription	Ovary	ovary
14	chr6:74209000-74224800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:74209200-74225000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:74209800-74224200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:74210400-74224000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:74210400-74224000	Weak transcription	Small Intestine	intestine
19	chr6:74210800-74224600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:74211400-74225000	Weak transcription	Esophagus	oesophagus
21	chr6:74211600-74223600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:74211600-74224600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:74211600-74224600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:74211600-74224600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:74211600-74224600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:74211600-74224600	Weak transcription	Fetal Kidney	kidney
27	chr6:74211600-74224600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:74211600-74224600	Weak transcription	Hela-S3	cervix
29	chr6:74211600-74224600	Weak transcription	HUVEC	blood vessel
30	chr6:74211600-74224600	Weak transcription	NH-A	brain
31	chr6:74211600-74224600	Weak transcription	NHEK	skin
32	chr6:74211600-74224800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:74211600-74224800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:74211600-74225000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:74211600-74225000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:74211600-74225000	Weak transcription	Brain Substantia Nigra	brain
37	chr6:74211600-74225000	Weak transcription	HSMMtube	muscle
38	chr6:74211600-74225800	Weak transcription	Aorta	Aorta
39	chr6:74211600-74226000	Weak transcription	HepG2	liver
40	chr6:74211800-74224200	Weak transcription	Left Ventricle	heart
41	chr6:74211800-74224200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:74211800-74224600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:74211800-74224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:74211800-74224600	Weak transcription	NHDF-Ad	bronchial
45	chr6:74211800-74224800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:74211800-74224800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:74211800-74224800	Weak transcription	HMEC	breast
48	chr6:74211800-74225000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:74211800-74225800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:74211800-74226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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