Variant report

Variant	rs479248
Chromosome Location	chr6:74290317-74290318
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74289861..74290649-chr6:74320011..74320830,2	K562	blood:
2	chr6:74240266..74241982-chr6:74289270..74292140,2	K562	blood:
3	chr17:58601960..58604487-chr6:74288896..74291198,2	MCF-7	breast:
4	chr6:74288220..74292842-chr6:74293561..74299022,14	K562	blood:
5	chr6:74224085..74235157-chr6:74287002..74297560,44	MCF-7	breast:
6	chr6:74284448..74288356-chr6:74288794..74290756,3	K562	blood:
7	chr6:74269117..74271723-chr6:74288666..74291103,2	K562	blood:
8	chr6:74273534..74278713-chr6:74287099..74290342,5	K562	blood:
9	chr6:74287590..74292040-chr6:74293648..74296536,4	MCF-7	breast:
10	chr6:74220978..74235626-chr6:74283533..74299827,68	K562	blood:
11	chr6:74289400..74291703-chr6:74315095..74317894,2	K562	blood:
12	chr3:49208726..49209579-chr6:74290200..74290971,2	HCT-116	colon:
13	chr6:74246086..74248922-chr6:74289757..74291955,2	MCF-7	breast:
14	chr6:74289354..74292208-chr6:74297018..74299790,3	MCF-7	breast:
15	chr6:74233223..74234154-chr6:74290069..74290962,2	Hela-S3	cervix:
16	chr6:74278735..74283200-chr6:74288390..74290564,5	K562	blood:
17	chr6:74236575..74238816-chr6:74288971..74291408,2	K562	blood:
18	chr6:74222492..74235445-chr6:74283533..74292948,42	K562	blood:
19	chr6:74223949..74234010-chr6:74285694..74297775,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000223967	Chromatin interaction

Extended variants
information (count: 185 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:176)

rs_ID	r²[population]
rs1083740	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1083741	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12177538	0.85[EUR][1000 genomes]
rs12198468	1.00[JPT][hapmap]
rs1245279	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1245344	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1390080	1.00[JPT][hapmap]
rs16883973	0.88[EUR][1000 genomes]
rs16883979	0.85[EUR][1000 genomes]
rs1691341	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1691342	0.81[EUR][1000 genomes]
rs1691349	0.84[EUR][1000 genomes]
rs1691352	0.81[EUR][1000 genomes]
rs1691353	0.81[EUR][1000 genomes]
rs1703465	0.85[EUR][1000 genomes]
rs1703466	0.85[EUR][1000 genomes]
rs1713862	1.00[JPT][hapmap]
rs1741886	0.85[EUR][1000 genomes]
rs1741888	0.81[EUR][1000 genomes]
rs1741893	0.81[EUR][1000 genomes]
rs1741894	0.81[EUR][1000 genomes]
rs1741895	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1741899	0.83[EUR][1000 genomes]
rs1808000	0.83[EUR][1000 genomes]
rs1848523	1.00[CEU][hapmap]
rs1874231	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1972073	0.81[EUR][1000 genomes]
rs2643196	0.81[ASN][1000 genomes]
rs2753184	0.81[EUR][1000 genomes]
rs364734	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs371827	1.00[CEU][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes]
rs3757108	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4079357	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4302643	0.81[EUR][1000 genomes]
rs4708060	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4708072	0.81[EUR][1000 genomes]
rs4708073	0.83[EUR][1000 genomes]
rs472294	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs472300	0.81[EUR][1000 genomes]
rs473078	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs473921	0.81[EUR][1000 genomes]
rs474661	0.85[EUR][1000 genomes]
rs476838	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs477431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477820	0.81[EUR][1000 genomes]
rs478503	0.81[EUR][1000 genomes]
rs485349	0.85[EUR][1000 genomes]
rs487490	0.85[EUR][1000 genomes]
rs494807	0.82[EUR][1000 genomes]
rs5007648	0.83[EUR][1000 genomes]
rs5007649	0.83[EUR][1000 genomes]
rs5007650	0.83[EUR][1000 genomes]
rs5007651	0.83[EUR][1000 genomes]
rs5007652	0.83[EUR][1000 genomes]
rs504477	0.85[EUR][1000 genomes]
rs506157	0.85[EUR][1000 genomes]
rs506262	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs518566	0.85[EUR][1000 genomes]
rs520589	0.85[EUR][1000 genomes]
rs523883	1.00[JPT][hapmap]
rs525041	0.85[EUR][1000 genomes]
rs525044	0.85[EUR][1000 genomes]
rs527606	0.85[EUR][1000 genomes]
rs534211	0.85[EUR][1000 genomes]
rs535902	1.00[JPT][hapmap]
rs537379	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540197	0.81[EUR][1000 genomes]
rs541178	1.00[JPT][hapmap]
rs543642	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs555151	0.81[EUR][1000 genomes]
rs555286	0.81[EUR][1000 genomes]
rs555840	0.81[EUR][1000 genomes]
rs555957	0.85[EUR][1000 genomes]
rs558641	0.85[EUR][1000 genomes]
rs558839	0.85[EUR][1000 genomes]
rs559843	0.81[EUR][1000 genomes]
rs562557	0.85[EUR][1000 genomes]
rs564364	0.85[EUR][1000 genomes]
rs567200	0.86[EUR][1000 genomes]
rs567727	0.81[EUR][1000 genomes]
rs570050	0.81[EUR][1000 genomes]
rs572147	0.81[EUR][1000 genomes]
rs57315094	0.83[EUR][1000 genomes]
rs580531	0.85[EUR][1000 genomes]
rs583149	0.85[EUR][1000 genomes]
rs58417654	0.83[EUR][1000 genomes]
rs584571	0.85[EUR][1000 genomes]
rs58783392	0.83[EUR][1000 genomes]
rs588852	0.81[EUR][1000 genomes]
rs592752	0.88[EUR][1000 genomes]
rs595884	0.85[EUR][1000 genomes]
rs596414	0.85[EUR][1000 genomes]
rs598121	0.84[EUR][1000 genomes]
rs60551677	0.82[EUR][1000 genomes]
rs605857	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606742	0.81[EUR][1000 genomes]
rs606793	0.81[EUR][1000 genomes]
rs607132	0.81[EUR][1000 genomes]
rs607667	0.81[EUR][1000 genomes]
rs608557	0.84[EUR][1000 genomes]
rs609439	0.85[EUR][1000 genomes]
rs609790	0.85[EUR][1000 genomes]
rs609829	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs610260	0.85[EUR][1000 genomes]
rs611580	0.85[EUR][1000 genomes]
rs623310	0.81[EUR][1000 genomes]
rs624632	0.81[EUR][1000 genomes]
rs625086	0.85[EUR][1000 genomes]
rs625478	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs625512	0.81[EUR][1000 genomes]
rs628732	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636166	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs636605	0.85[EUR][1000 genomes]
rs639256	0.81[EUR][1000 genomes]
rs6453684	0.85[EUR][1000 genomes]
rs651981	0.81[EUR][1000 genomes]
rs653781	0.81[EUR][1000 genomes]
rs654973	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs656748	0.85[EUR][1000 genomes]
rs657212	0.85[EUR][1000 genomes]
rs658475	1.00[JPT][hapmap]
rs673176	0.85[EUR][1000 genomes]
rs673511	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs674482	0.85[EUR][1000 genomes]
rs674708	1.00[JPT][hapmap]
rs674938	0.85[EUR][1000 genomes]
rs674988	0.88[EUR][1000 genomes]
rs674989	0.85[EUR][1000 genomes]
rs676704	0.85[EUR][1000 genomes]
rs677073	0.85[EUR][1000 genomes]
rs678054	0.85[EUR][1000 genomes]
rs680391	0.85[EUR][1000 genomes]
rs685491	0.85[EUR][1000 genomes]
rs686317	0.85[EUR][1000 genomes]
rs687210	0.85[EUR][1000 genomes]
rs6907936	1.00[JPT][hapmap]
rs6930178	0.85[EUR][1000 genomes]
rs6930465	0.88[EUR][1000 genomes]
rs6940526	0.85[EUR][1000 genomes]
rs6940706	0.85[EUR][1000 genomes]
rs6940886	0.85[EUR][1000 genomes]
rs71542212	0.85[EUR][1000 genomes]
rs73454523	0.81[EUR][1000 genomes]
rs766708	0.81[EUR][1000 genomes]
rs7739206	0.83[EUR][1000 genomes]
rs7747069	0.85[EUR][1000 genomes]
rs7758825	0.85[EUR][1000 genomes]
rs7759157	0.85[EUR][1000 genomes]
rs7764560	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7764768	0.82[EUR][1000 genomes]
rs7764983	0.85[EUR][1000 genomes]
rs780062	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]
rs780063	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs780069	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs780070	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903515	0.81[EUR][1000 genomes]
rs9293930	1.00[JPT][hapmap]
rs9293932	0.82[EUR][1000 genomes]
rs9293933	0.85[EUR][1000 genomes]
rs9341424	1.00[JPT][hapmap]
rs9352000	1.00[JPT][hapmap]
rs9446947	0.85[EUR][1000 genomes]
rs9446949	0.81[EUR][1000 genomes]
rs9446952	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9446953	0.85[EUR][1000 genomes]
rs9446954	0.85[EUR][1000 genomes]
rs9446955	0.85[EUR][1000 genomes]
rs9446957	0.85[EUR][1000 genomes]
rs9446958	0.85[EUR][1000 genomes]
rs9446960	0.81[EUR][1000 genomes]
rs9446961	0.85[EUR][1000 genomes]
rs9446962	0.85[EUR][1000 genomes]
rs9446964	0.83[EUR][1000 genomes]
rs9446966	0.85[EUR][1000 genomes]
rs9446973	0.84[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
rs479248	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74287200-74290800	Enhancers	Fetal Heart	heart
2	chr6:74287400-74290400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr6:74287400-74290400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:74288000-74296000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:74288600-74290400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:74289000-74290400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:74289000-74290400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:74289000-74290400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:74289000-74290800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:74289000-74291000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:74289000-74291000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:74289000-74291000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:74289000-74291000	Enhancers	Esophagus	oesophagus
14	chr6:74289200-74290600	Enhancers	Fetal Thymus	thymus
15	chr6:74289200-74290600	Enhancers	Small Intestine	intestine
16	chr6:74289200-74290800	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:74289200-74291000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:74289400-74290400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:74289400-74290600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:74289400-74290600	Active TSS	HSMMtube	muscle
21	chr6:74289400-74290800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:74289400-74294800	Weak transcription	Pancreas	Pancrea
23	chr6:74289400-74302200	Weak transcription	Spleen	Spleen
24	chr6:74289400-74304000	Weak transcription	Right Ventricle	heart
25	chr6:74289600-74290400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:74289600-74290400	Weak transcription	Left Ventricle	heart
27	chr6:74289600-74290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:74289600-74290600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:74289600-74290600	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:74289600-74290600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:74289600-74290600	Active TSS	HSMM	muscle
32	chr6:74289600-74290800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:74289600-74290800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:74289600-74294800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:74289600-74295000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:74289600-74309600	Weak transcription	Lung	lung
37	chr6:74289600-74323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:74289800-74290400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:74289800-74290400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:74289800-74290400	Active TSS	Adipose Nuclei	Adipose
41	chr6:74289800-74290400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:74289800-74290600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr6:74289800-74290600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:74289800-74290600	Active TSS	Brain Substantia Nigra	brain
45	chr6:74289800-74290600	Active TSS	NHLF	lung
46	chr6:74289800-74290800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr6:74289800-74290800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:74289800-74290800	Active TSS	Right Atrium	heart
49	chr6:74289800-74290800	Active TSS	A549	lung
50	chr6:74289800-74291000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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