Variant report

Variant	rs780062
Chromosome Location	chr6:74291544-74291545
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74240266..74241982-chr6:74289270..74292140,2	K562	blood:
2	chr6:74288220..74292842-chr6:74293561..74299022,14	K562	blood:
3	chr6:74224085..74235157-chr6:74287002..74297560,44	MCF-7	breast:
4	chr6:74286237..74288439-chr6:74291393..74292991,3	K562	blood:
5	chr6:74287590..74292040-chr6:74293648..74296536,4	MCF-7	breast:
6	chr6:74220978..74235626-chr6:74283533..74299827,68	K562	blood:
7	chr6:74289400..74291703-chr6:74315095..74317894,2	K562	blood:
8	chr6:74246086..74248922-chr6:74289757..74291955,2	MCF-7	breast:
9	chr6:74272516..74275188-chr6:74290634..74292979,3	K562	blood:
10	chr6:74289354..74292208-chr6:74297018..74299790,3	MCF-7	breast:
11	chr6:74164533..74167289-chr6:74290489..74292657,2	MCF-7	breast:
12	chr6:74222492..74235445-chr6:74283533..74292948,42	K562	blood:
13	chr6:74223949..74234010-chr6:74285694..74297775,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs1083740	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1083741	0.96[EUR][1000 genomes]
rs12177538	0.81[EUR][1000 genomes]
rs12198468	1.00[JPT][hapmap]
rs1245279	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1245344	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390080	1.00[JPT][hapmap]
rs16883973	0.84[EUR][1000 genomes]
rs16883979	0.81[EUR][1000 genomes]
rs1691341	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1691342	0.84[EUR][1000 genomes]
rs1691349	0.88[EUR][1000 genomes]
rs1691352	0.84[EUR][1000 genomes]
rs1691353	0.84[EUR][1000 genomes]
rs1703461	0.83[EUR][1000 genomes]
rs1703465	0.81[EUR][1000 genomes]
rs1703466	0.81[EUR][1000 genomes]
rs1713862	1.00[JPT][hapmap]
rs1741886	0.81[EUR][1000 genomes]
rs1741893	0.84[EUR][1000 genomes]
rs1741894	0.84[EUR][1000 genomes]
rs1741895	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1848523	0.82[EUR][1000 genomes]
rs1874231	0.84[EUR][1000 genomes]
rs1972073	0.84[EUR][1000 genomes]
rs2643196	0.81[EUR][1000 genomes]
rs2753184	0.85[EUR][1000 genomes]
rs364734	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs371827	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs3757108	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4079357	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4708060	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs472294	0.88[EUR][1000 genomes]
rs472300	0.84[EUR][1000 genomes]
rs473078	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs473921	0.84[EUR][1000 genomes]
rs474661	0.81[EUR][1000 genomes]
rs476838	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs477431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs477820	0.84[EUR][1000 genomes]
rs478503	0.84[EUR][1000 genomes]
rs479248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs485349	0.81[EUR][1000 genomes]
rs487490	0.81[EUR][1000 genomes]
rs490454	0.83[EUR][1000 genomes]
rs493068	0.81[EUR][1000 genomes]
rs494807	0.86[EUR][1000 genomes]
rs494841	0.83[EUR][1000 genomes]
rs504477	0.81[EUR][1000 genomes]
rs506157	0.81[EUR][1000 genomes]
rs506262	0.88[EUR][1000 genomes]
rs518566	0.81[EUR][1000 genomes]
rs520589	0.81[EUR][1000 genomes]
rs523883	1.00[JPT][hapmap]
rs525041	0.81[EUR][1000 genomes]
rs525044	0.81[EUR][1000 genomes]
rs527606	0.81[EUR][1000 genomes]
rs534211	0.81[EUR][1000 genomes]
rs535902	1.00[JPT][hapmap]
rs537379	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540197	0.84[EUR][1000 genomes]
rs541178	1.00[JPT][hapmap]
rs543642	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs555151	0.84[EUR][1000 genomes]
rs555286	0.84[EUR][1000 genomes]
rs555957	0.81[EUR][1000 genomes]
rs558641	0.81[EUR][1000 genomes]
rs558839	0.81[EUR][1000 genomes]
rs559843	0.84[EUR][1000 genomes]
rs562557	0.81[EUR][1000 genomes]
rs564364	0.81[EUR][1000 genomes]
rs567200	0.83[EUR][1000 genomes]
rs567727	0.84[EUR][1000 genomes]
rs568422	0.81[EUR][1000 genomes]
rs570050	0.84[EUR][1000 genomes]
rs572147	0.84[EUR][1000 genomes]
rs580531	0.81[EUR][1000 genomes]
rs583149	0.81[EUR][1000 genomes]
rs584571	0.81[EUR][1000 genomes]
rs588852	0.84[EUR][1000 genomes]
rs592752	0.84[EUR][1000 genomes]
rs595884	0.81[EUR][1000 genomes]
rs596414	0.81[EUR][1000 genomes]
rs598121	0.88[EUR][1000 genomes]
rs60551677	0.86[EUR][1000 genomes]
rs605857	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606742	0.84[EUR][1000 genomes]
rs606793	0.84[EUR][1000 genomes]
rs607132	0.84[EUR][1000 genomes]
rs607667	0.84[EUR][1000 genomes]
rs608557	0.88[EUR][1000 genomes]
rs609439	0.81[EUR][1000 genomes]
rs609790	0.81[EUR][1000 genomes]
rs609829	0.81[EUR][1000 genomes]
rs610260	0.81[EUR][1000 genomes]
rs611580	0.81[EUR][1000 genomes]
rs622967	0.83[EUR][1000 genomes]
rs623310	0.84[EUR][1000 genomes]
rs625086	0.81[EUR][1000 genomes]
rs625478	1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs628732	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs636166	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs636605	0.81[EUR][1000 genomes]
rs639256	0.84[EUR][1000 genomes]
rs6453684	0.81[EUR][1000 genomes]
rs651981	0.84[EUR][1000 genomes]
rs653781	0.84[EUR][1000 genomes]
rs654973	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs656748	0.81[EUR][1000 genomes]
rs657212	0.81[EUR][1000 genomes]
rs658475	1.00[JPT][hapmap]
rs673176	0.81[EUR][1000 genomes]
rs673511	0.81[EUR][1000 genomes]
rs674482	0.81[EUR][1000 genomes]
rs674708	1.00[JPT][hapmap]
rs674938	0.81[EUR][1000 genomes]
rs674988	0.84[EUR][1000 genomes]
rs674989	0.81[EUR][1000 genomes]
rs676704	0.81[EUR][1000 genomes]
rs677073	0.81[EUR][1000 genomes]
rs678054	0.81[EUR][1000 genomes]
rs680391	0.81[EUR][1000 genomes]
rs685491	0.81[EUR][1000 genomes]
rs686317	0.81[EUR][1000 genomes]
rs687210	0.81[EUR][1000 genomes]
rs6907936	1.00[JPT][hapmap]
rs6930178	0.81[EUR][1000 genomes]
rs6930465	0.84[EUR][1000 genomes]
rs6940526	0.81[EUR][1000 genomes]
rs6940706	0.81[EUR][1000 genomes]
rs6940886	0.81[EUR][1000 genomes]
rs71542212	0.81[EUR][1000 genomes]
rs73454523	0.84[EUR][1000 genomes]
rs7747069	0.81[EUR][1000 genomes]
rs7758825	0.81[EUR][1000 genomes]
rs7759157	0.81[EUR][1000 genomes]
rs7764560	0.81[EUR][1000 genomes]
rs7764983	0.81[EUR][1000 genomes]
rs780063	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs780069	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780070	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs903515	0.84[EUR][1000 genomes]
rs9293930	1.00[JPT][hapmap]
rs9293933	0.81[EUR][1000 genomes]
rs9341424	1.00[JPT][hapmap]
rs9352000	1.00[JPT][hapmap]
rs9446947	0.81[EUR][1000 genomes]
rs9446949	0.84[EUR][1000 genomes]
rs9446952	0.81[EUR][1000 genomes]
rs9446953	0.81[EUR][1000 genomes]
rs9446954	0.81[EUR][1000 genomes]
rs9446955	0.81[EUR][1000 genomes]
rs9446957	0.81[EUR][1000 genomes]
rs9446958	0.81[EUR][1000 genomes]
rs9446961	0.81[EUR][1000 genomes]
rs9446962	0.81[EUR][1000 genomes]
rs9446966	0.81[EUR][1000 genomes]
rs9446973	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs780062	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74288000-74296000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:74289400-74294800	Weak transcription	Pancreas	Pancrea
3	chr6:74289400-74302200	Weak transcription	Spleen	Spleen
4	chr6:74289400-74304000	Weak transcription	Right Ventricle	heart
5	chr6:74289600-74294800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:74289600-74295000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:74289600-74309600	Weak transcription	Lung	lung
8	chr6:74289600-74323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:74289800-74301400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:74290400-74294800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:74290600-74294600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:74290600-74294800	Weak transcription	Fetal Thymus	thymus
13	chr6:74290600-74295000	Weak transcription	Primary T cells from cord blood	blood
14	chr6:74290600-74305800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:74290600-74318400	Weak transcription	Small Intestine	intestine
16	chr6:74290600-74338800	Weak transcription	Ovary	ovary
17	chr6:74290800-74291600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:74290800-74294800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:74290800-74294800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:74290800-74294800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:74290800-74294800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:74290800-74294800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:74290800-74294800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:74290800-74295000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:74290800-74295000	Weak transcription	Fetal Kidney	kidney
26	chr6:74290800-74295200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:74291000-74291600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:74291000-74291600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:74291000-74291600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:74291000-74291600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:74291000-74291600	Enhancers	Hela-S3	cervix
32	chr6:74291000-74294400	Weak transcription	Primary B cells from cord blood	blood
33	chr6:74291000-74294400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:74291000-74294600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:74291000-74294800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:74291000-74294800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:74291000-74294800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:74291000-74294800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:74291000-74294800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:74291000-74294800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:74291000-74294800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:74291000-74294800	Weak transcription	Liver	Liver
43	chr6:74291000-74294800	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:74291000-74294800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:74291000-74294800	Weak transcription	Fetal Intestine Small	intestine
46	chr6:74291000-74294800	Weak transcription	Fetal Lung	lung
47	chr6:74291000-74294800	Weak transcription	Placenta	Placenta
48	chr6:74291000-74294800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:74291000-74294800	Weak transcription	Stomach Mucosa	stomach
50	chr6:74291000-74294800	Weak transcription	Stomach Smooth Muscle	stomach

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