Variant report

Variant	rs9341424
Chromosome Location	chr6:74170860-74170861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:74170750-74172266	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr6:74170840-74170990	HCPEpiC	choroid plexus:	n/a	chr6:74170847-74170868
3	PML	chr6:74170844-74170998	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:74170778-74172020	HUVEC	blood vessel:	n/a	n/a
5	JUND	chr6:74170675-74172132	GM12878	blood:	n/a	chr6:74171847-74171856 chr6:74171431-74171440
6	CTCF	chr6:74170840-74170990	GM06990	blood:	n/a	chr6:74170847-74170868
7	CTCF	chr6:74170740-74171030	NHDF-neo	bronchial:	n/a	chr6:74170847-74170868
8	CTCF	chr6:74170855-74171107	GM12878	blood:	n/a	n/a
9	CTCF	chr6:74170860-74171010	GM12874	blood:	n/a	n/a
10	CTCF	chr6:74170820-74170970	MCF-7	breast:	n/a	chr6:74170847-74170868
11	POLR2A	chr6:74170856-74172089	GM19099	blood:	n/a	n/a
12	CTCF	chr6:74170740-74170890	BE2_C	brain:	n/a	chr6:74170847-74170868
13	POLR2A	chr6:74170816-74172008	GM12891	blood:	n/a	n/a
14	CTCF	chr6:74170860-74171010	GM12869	blood:	n/a	n/a
15	POLR2A	chr6:74170814-74172264	GM12892	blood:	n/a	n/a
16	RAD21	chr6:74170815-74171085	Hela-S3	cervix:	n/a	chr6:74170846-74170865
17	CTCF	chr6:74170860-74171010	GM12864	blood:	n/a	n/a
18	MAX	chr6:74170805-74171119	K562	blood:	n/a	n/a
19	POLR2A	chr6:74170814-74172110	Raji	blood:	n/a	n/a
20	GATA2	chr6:74170709-74171080	SH-SY5Y	brain:	n/a	chr6:74170864-74170871 chr6:74170887-74170899 chr6:74170887-74170894 chr6:74170885-74170901
21	HA-E2F1	chr6:74170843-74172150	MCF-7	breast:	n/a	chr6:74171843-74171855 chr6:74171429-74171438
22	POLR2A	chr6:74169765-74172235	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr6:74170709-74171119	PFSK-1	brain:	n/a	n/a
24	CUX1	chr6:74170753-74171105	K562	blood:	n/a	n/a
25	CTCF	chr6:74170860-74171010	HMEC	breast:	n/a	n/a
26	POLR2A	chr6:74170706-74172189	PANC-1	pancreas:	n/a	n/a
27	CTCF	chr6:74170810-74171113	K562	blood:	n/a	chr6:74170847-74170868
28	POLR2A	chr6:74170851-74172161	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr6:74170860-74171010	GM12872	blood:	n/a	n/a
30	MAX	chr6:74170721-74171181	K562	blood:	n/a	n/a
31	RUNX3	chr6:74170781-74171177	GM12878	blood:	n/a	n/a
32	CUX1	chr6:74170774-74171039	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:74170804-74171179	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:74170787-74172177	HepG2	liver:	n/a	n/a
35	POLR2A	chr6:74170828-74171168	HCT-116	colon:	n/a	n/a
36	CTCF	chr6:74170720-74170870	GM12873	blood:	n/a	chr6:74170847-74170868
37	CTCF	chr6:74170860-74171010	HBMEC	blood vessel:	n/a	n/a
38	NR2F2	chr6:74170829-74172190	K562	blood:	n/a	chr6:74170969-74170984
39	CTCF	chr6:74170840-74170990	HUVEC	blood vessel:	n/a	chr6:74170847-74170868
40	CTCF	chr6:74170820-74170970	HepG2	liver:	n/a	chr6:74170847-74170868
41	GATA3	chr6:74170708-74171186	MCF-7	breast:	n/a	chr6:74170864-74170871 chr6:74170887-74170899 chr6:74170887-74170894 chr6:74170885-74170901
42	SREBP1	chr6:74170746-74172046	GM12878	blood:	n/a	n/a
43	GATA3	chr6:74170753-74171301	MCF-7	breast:	n/a	chr6:74170864-74170871 chr6:74170887-74170899 chr6:74170887-74170894 chr6:74170885-74170901
44	CTCF	chr6:74170860-74171010	GM12873	blood:	n/a	n/a
45	RUNX3	chr6:74170793-74171178	GM12878	blood:	n/a	n/a
46	CTCF	chr6:74170860-74171010	GM12875	blood:	n/a	n/a
47	CTCF	chr6:74170760-74170910	HAc	cerebellar:	n/a	chr6:74170847-74170868
48	GATA1	chr6:74170790-74171976	PBDE	blood:	n/a	chr6:74170864-74170871 chr6:74170887-74170899 chr6:74170887-74170894 chr6:74170885-74170901
49	CTCF	chr6:74170860-74171010	NHEK	skin:	n/a	n/a
50	CTCF	chr6:74170820-74170970	SAEC	small airway:	n/a	chr6:74170847-74170868

No.	Distal block	Cell Line	Cell type
1	chr6:74170147..74173171-chr6:74228405..74233047,5	K562	blood:
2	chr6:74169971..74171514-chr6:74363161..74365275,2	K562	blood:
3	chr6:74161054..74162803-chr6:74170149..74171814,3	K562	blood:
4	6:74000304-74012200..6:74160392-74184826	K562	blood:
5	chr6:74169192..74174230-chr6:74229143..74231785,9	K562	blood:
6	chr6:74160549..74162466-chr6:74170605..74172336,2	MCF-7	breast:
7	chr6:74169360..74174580-chr6:74228668..74231530,6	MCF-7	breast:
8	chr6:74101120..74105028-chr6:74169928..74173303,3	K562	blood:
9	chr6:74160479..74164788-chr6:74167921..74174562,8	MCF-7	breast:
10	chr6:74161054..74162803-chr6:74170149..74171792,2	K562	blood:
11	chr6:74170014..74172890-chr6:74363161..74365164,3	K562	blood:

Variant related genes	Relation type
MTO1	TF binding region
RNU6-975P	TF binding region
ENSG00000080007	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000234882	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000203907	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12198468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1245345	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245346	0.81[EUR][1000 genomes]
rs1390080	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]
rs1703461	1.00[CEU][hapmap]
rs1713862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741886	1.00[CEU][hapmap]
rs2643196	0.90[ASN][1000 genomes]
rs28576277	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs371827	0.89[JPT][hapmap]
rs4708060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474661	1.00[CEU][hapmap]
rs479248	1.00[JPT][hapmap]
rs494841	1.00[CEU][hapmap]
rs506157	1.00[CEU][hapmap]
rs516203	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs523883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527606	1.00[CEU][hapmap]
rs535902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs541178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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]
rs606263	1.00[JPT][hapmap]
rs608026	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs609790	1.00[CEU][hapmap]
rs609829	1.00[CEU][hapmap]
rs610260	1.00[CEU][hapmap]
rs611580	1.00[CEU][hapmap]
rs621493	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs625478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs625512	1.00[CEU][hapmap]
rs636605	1.00[CEU][hapmap]
rs649909	0.84[ASN][1000 genomes]
rs654973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs657212	1.00[CEU][hapmap]
rs658475	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]
rs674708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678054	1.00[CEU][hapmap]
rs679272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs7749897	0.81[EUR][1000 genomes];0.93[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];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9293933	1.00[CEU][hapmap]
rs9352000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9352002	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9352007	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9360689	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9446904	1.00[ASN][1000 genomes]
rs9446952	1.00[CEU][hapmap]
rs9446955	1.00[CEU][hapmap]
rs9446957	1.00[CEU][hapmap]
rs9446964	1.00[CEU][hapmap]
rs951332	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9341424	MTO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74164800-74171200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:74170400-74171000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr6:74170400-74171400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:74170400-74172400	Active TSS	Dnd41	blood
5	chr6:74170600-74171000	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr6:74170600-74171000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr6:74170600-74171000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr6:74170600-74171000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr6:74170600-74171000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:74170600-74171000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr6:74170600-74171000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:74170600-74171000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:74170600-74171000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:74170600-74171600	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:74170600-74172200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:74170600-74172400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:74170600-74172400	Active TSS	Brain Germinal Matrix	brain
18	chr6:74170600-74172400	Active TSS	Fetal Stomach	stomach
19	chr6:74170600-74172600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:74170600-74172600	Active TSS	Primary T cells from cord blood	blood
21	chr6:74170600-74172600	Active TSS	Duodenum Mucosa	Duodenum
22	chr6:74170600-74172600	Active TSS	Right Ventricle	heart
23	chr6:74170600-74172600	Active TSS	Thymus	Thymus
24	chr6:74170600-74172600	Active TSS	HSMM	muscle
25	chr6:74170600-74172800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:74170600-74173000	Active TSS	Hela-S3	cervix
27	chr6:74170800-74171000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:74170800-74171000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:74170800-74171000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:74170800-74171000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:74170800-74171000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:74170800-74171000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr6:74170800-74171000	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr6:74170800-74171000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr6:74170800-74171000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:74170800-74171000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:74170800-74171000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr6:74170800-74171000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:74170800-74171000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:74170800-74171000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:74170800-74171000	Flanking Active TSS	Liver	Liver
42	chr6:74170800-74171000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr6:74170800-74171000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:74170800-74171000	ZNF genes & repeats	Fetal Brain Male	brain
45	chr6:74170800-74171000	Flanking Active TSS	Fetal Brain Female	brain
46	chr6:74170800-74171000	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr6:74170800-74171000	Flanking Active TSS	Placenta	Placenta
48	chr6:74170800-74171000	Flanking Active TSS	Fetal Thymus	thymus
49	chr6:74170800-74171000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr6:74170800-74171000	Flanking Active TSS	HepG2	liver

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