Variant report

Variant	rs584078
Chromosome Location	chr6:74335621-74335622
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74221323..74236726-chr6:74306065..74338770,101	K562	blood:
2	chr6:74230217..74232050-chr6:74335341..74337314,2	MCF-7	breast:
3	chr6:74224257..74227085-chr6:74333037..74337394,5	K562	blood:

Variant related genes	Relation type
ENSG00000223967	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000229862	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12198468	0.82[CEU][hapmap]
rs1390080	0.82[CEU][hapmap]
rs1691341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1691343	0.88[JPT][hapmap]
rs1703461	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1713862	0.82[CEU][hapmap]
rs1741886	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1741889	0.87[JPT][hapmap]
rs1741895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1848523	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874231	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs364734	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3757108	1.00[JPT][hapmap]
rs382041	0.88[JPT][hapmap]
rs4032317	0.87[JPT][hapmap]
rs4079357	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4708072	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs4708073	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs472294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs473078	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs474661	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs476838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs485802	0.87[JPT][hapmap]
rs494841	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs495385	1.00[YRI][hapmap]
rs506157	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs506262	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs523883	0.82[CEU][hapmap]
rs527606	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs535902	0.82[CEU][hapmap]
rs541178	0.82[CEU][hapmap]
rs543642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs555840	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs570050	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs580531	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs583149	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs584571	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs609790	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs609829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs610260	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs611580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs625512	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs629381	0.87[JPT][hapmap]
rs636166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs636605	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs642651	0.87[JPT][hapmap]
rs657212	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs658475	0.82[CEU][hapmap]
rs673511	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs674708	0.82[CEU][hapmap]
rs678054	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs685491	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs686317	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs687210	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7764560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7764983	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9293932	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs9293933	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9341424	0.82[CEU][hapmap]
rs9446952	0.81[JPT][hapmap]
rs9446955	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9446957	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs9446964	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
9	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv886160	chr6:74305276-74341589	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs584078	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74290600-74338800	Weak transcription	Ovary	ovary
2	chr6:74296400-74354800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:74296400-74354800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:74296400-74355000	Weak transcription	Fetal Brain Male	brain
5	chr6:74296600-74344000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:74297000-74361800	Weak transcription	GM12878-XiMat	blood
7	chr6:74303400-74355000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:74307200-74362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:74307600-74356400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:74308000-74340200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:74311200-74355000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:74314200-74362800	Weak transcription	Stomach Mucosa	stomach
13	chr6:74314400-74346400	Weak transcription	Psoas Muscle	Psoas
14	chr6:74315200-74348800	Weak transcription	HMEC	breast
15	chr6:74315400-74345200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:74315600-74362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:74316200-74347000	Strong transcription	Fetal Intestine Small	intestine
18	chr6:74316400-74349200	Weak transcription	HUVEC	blood vessel
19	chr6:74316600-74355000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:74318400-74350000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:74318400-74355000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:74318800-74355200	Weak transcription	Colonic Mucosa	Colon
23	chr6:74319000-74341200	Weak transcription	NH-A	brain
24	chr6:74319600-74354800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:74319800-74340000	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:74319800-74354800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:74320400-74340200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:74320800-74341200	Weak transcription	Brain Angular Gyrus	brain
29	chr6:74322800-74341200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:74324600-74362800	Weak transcription	Pancreas	Pancrea
31	chr6:74324800-74338800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:74324800-74339600	Weak transcription	Primary B cells from cord blood	blood
33	chr6:74324800-74342200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:74324800-74361600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:74325000-74335800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:74325000-74337600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:74325000-74337600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:74325000-74337600	Weak transcription	Spleen	Spleen
39	chr6:74325000-74337800	Weak transcription	Thymus	Thymus
40	chr6:74325000-74338400	Weak transcription	HepG2	liver
41	chr6:74325000-74338800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:74325000-74340200	Weak transcription	Fetal Brain Female	brain
43	chr6:74325000-74341200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:74325000-74341200	Weak transcription	Esophagus	oesophagus
45	chr6:74325000-74342200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:74325000-74342200	Weak transcription	Brain Germinal Matrix	brain
47	chr6:74325000-74344000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:74325000-74346000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:74325000-74348800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:74325000-74349400	Weak transcription	Rectal Smooth Muscle	rectum

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