Variant report

Variant	rs1713862
Chromosome Location	chr6:74171467-74171468
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:408)
CpG islands
(count:122)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:408 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr6:74171255-74172021	K562	blood:	n/a	n/a
2	SIN3AK20	chr6:74171418-74171800	A549	lung:	n/a	n/a
3	MTA3	chr6:74171341-74171966	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr6:74171424-74171642	A549	lung:	n/a	n/a
5	MXI1	chr6:74170750-74172266	SK-N-SH	brain:	n/a	n/a
6	REST	chr6:74171131-74172209	H1-neurons	neurons:	n/a	chr6:74171803-74171813
7	ZNF143	chr6:74171317-74172079	GM12878	blood:	n/a	n/a
8	FOXP2	chr6:74171362-74171675	SK-N-MC	brain:	n/a	n/a
9	YY1	chr6:74171290-74171906	NT2-D1	testis:	n/a	n/a
10	POLR2A	chr6:74171137-74171860	U87	brain:	n/a	n/a
11	CREB1	chr6:74171347-74171671	A549	lung:	n/a	n/a
12	GTF2F1	chr6:74170999-74172043	Hela-S3	cervix:	n/a	n/a
13	TAF1	chr6:74171283-74171682	SK-N-SH	brain:	n/a	n/a
14	HCFC1	chr6:74171307-74172307	Hela-S3	cervix:	n/a	n/a
15	YY1	chr6:74171333-74172178	ECC-1	luminal epithelium:	n/a	n/a
16	ELF1	chr6:74171315-74171741	HepG2	liver:	n/a	n/a
17	CEBPB	chr6:74171377-74171649	K562	blood:	n/a	n/a
18	TAF1	chr6:74171326-74171976	GM12892	blood:	n/a	n/a
19	EP300	chr6:74170937-74171603	GM12878	blood:	n/a	n/a
20	EP300	chr6:74171166-74171561	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:74171261-74171954	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr6:74171314-74172094	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr6:74170778-74172020	HUVEC	blood vessel:	n/a	n/a
24	TAF1	chr6:74171303-74171974	MCF-7	breast:	n/a	n/a
25	CEBPB	chr6:74171331-74171903	MCF-7	breast:	n/a	n/a
26	TAF1	chr6:74171344-74171938	HepG2	liver:	n/a	n/a
27	NFYA	chr6:74171323-74171754	Hela-S3	cervix:	n/a	chr6:74171427-74171442 chr6:74171427-74171442 chr6:74171429-74171439
28	ZNF143	chr6:74171382-74171828	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr6:74171356-74171753	A549	lung:	n/a	n/a
30	MAX	chr6:74171421-74171886	A549	lung:	n/a	n/a
31	NFYB	chr6:74171287-74172052	K562	blood:	n/a	chr6:74171424-74171439 chr6:74171427-74171442 chr6:74171427-74171442 chr6:74171429-74171439
32	GTF2F1	chr6:74171353-74171596	K562	blood:	n/a	n/a
33	JUND	chr6:74170675-74172132	GM12878	blood:	n/a	chr6:74171847-74171856 chr6:74171431-74171440
34	POLR2A	chr6:74171328-74171897	A549	lung:	n/a	n/a
35	ARID3A	chr6:74171335-74171775	HepG2	liver:	n/a	n/a
36	YY1	chr6:74171285-74172011	GM12878	blood:	n/a	n/a
37	CEBPB	chr6:74171325-74171965	A549	lung:	n/a	n/a
38	MAX	chr6:74171330-74172194	Hela-S3	cervix:	n/a	n/a
39	TAF1	chr6:74171320-74171938	PFSK-1	brain:	n/a	n/a
40	TBP	chr6:74171278-74171832	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:74171154-74171881	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr6:74171293-74171893	GM10847	blood:	n/a	n/a
43	IRF1	chr6:74171284-74171729	K562	blood:	n/a	n/a
44	POLR2A	chr6:74171311-74172049	GM12878	blood:	n/a	n/a
45	YY1	chr6:74171303-74171840	HepG2	liver:	n/a	n/a
46	STAT5A	chr6:74171299-74171989	GM12878	blood:	n/a	n/a
47	TCF7L2	chr6:74171333-74172105	Hela-S3	cervix:	n/a	n/a
48	CEBPD	chr6:74171340-74171640	HepG2	liver:	n/a	n/a
49	TAF1	chr6:74171261-74171971	SK-N-SH	brain:	n/a	n/a
50	USF1	chr6:74171364-74171571	SK-N-SH_RA	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:74171430-74171480	HRCEpiC	kidney:	n/a
2	chr6:74171446-74171496	HCM	heart:	n/a
3	chr6:74171446-74171496	GM12892	blood:	n/a
4	chr6:74171446-74171496	SKMC	muscle:	n/a
5	chr6:74171430-74171480	GM12878	blood:	n/a
6	chr6:74171446-74171496	NB4	blood:	n/a
7	chr6:74171430-74171480	ECC-1	luminal epithelium:	n/a
8	chr6:74171446-74171496	GM06990	blood:	n/a
9	chr6:74171446-74171496	SK-N-SH	brain:	n/a
10	chr6:74171446-74171496	U87	brain:	n/a
11	chr6:74171430-74171480	MCF-7	breast:	n/a
12	chr6:74171430-74171480	AG04449	skin:	fetal
13	chr6:74171446-74171496	HNPCEpiC	eye:	n/a
14	chr6:74171430-74171480	HCF	heart:	n/a
15	chr6:74171446-74171496	HCT-116	colon:	n/a
16	chr6:74171430-74171480	MCF10A-Er-Src	breast:	n/a
17	chr6:74171430-74171480	SK-N-SH	brain:	n/a
18	chr6:74171430-74171480	BJ	skin:	n/a
19	chr6:74171430-74171480	HepG2	liver:	n/a
20	chr6:74171430-74171480	ProgFib	skin:	n/a
21	chr6:74171430-74171480	Hepatocyte	liver:	n/a
22	chr6:74171446-74171496	HepG2	liver:	n/a
23	chr6:74171446-74171496	Hepatocyte	liver:	n/a
24	chr6:74171430-74171480	NT2-D1	testis:	n/a
25	chr6:74171430-74171480	HEEpiC	esophagus:	n/a
26	chr6:74171430-74171480	AG09319	gingival:	n/a
27	chr6:74171446-74171496	MCF10A-Er-Src	breast:	n/a
28	chr6:74171430-74171480	U87	brain:	n/a
29	chr6:74171430-74171480	AoSMC	blood vessel:	n/a
30	chr6:74171430-74171480	GM19239	blood:	n/a
31	chr6:74171446-74171496	HEEpiC	esophagus:	n/a
32	chr6:74171430-74171480	K562	blood:	n/a
33	chr6:74171446-74171496	HL-60	blood:	n/a
34	chr6:74171430-74171480	Jurkat	blood:	n/a
35	chr6:74171446-74171496	HCF	heart:	n/a
36	chr6:74171446-74171496	H1-hESC	embryonic stem cell:	embryo
37	chr6:74171430-74171480	PFSK-1	brain:	n/a
38	chr6:74171446-74171496	AG10803	skin:	n/a
39	chr6:74171446-74171496	Caco-2	colon:	n/a
40	chr6:74171446-74171496	AoSMC	blood vessel:	n/a
41	chr6:74171430-74171480	HCPEpiC	choroid plexus:	n/a
42	chr6:74171446-74171496	GM12891	blood:	n/a
43	chr6:74171446-74171496	NT2-D1	testis:	n/a
44	chr6:74171430-74171480	HRE	kidney:	n/a
45	chr6:74171446-74171496	AG04449	skin:	fetal
46	chr6:74171446-74171496	AG09319	gingival:	n/a
47	chr6:74171430-74171480	HEK293	kidney:	embryo
48	chr6:74171446-74171496	ECC-1	luminal epithelium:	n/a
49	chr6:74171446-74171496	GM19239	blood:	n/a
50	chr6:74171446-74171496	AG09309	skin:	n/a

(count:11 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

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]
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]
rs9341424	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]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1713862	MTO1	Cis_1M	lymphoblastoid	RTeQTL
rs1713862	ENSG00000135297	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74170400-74172400	Active TSS	Dnd41	blood
2	chr6:74170600-74171600	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:74170600-74172200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:74170600-74172400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:74170600-74172400	Active TSS	Brain Germinal Matrix	brain
6	chr6:74170600-74172400	Active TSS	Fetal Stomach	stomach
7	chr6:74170600-74172600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr6:74170600-74172600	Active TSS	Primary T cells from cord blood	blood
9	chr6:74170600-74172600	Active TSS	Duodenum Mucosa	Duodenum
10	chr6:74170600-74172600	Active TSS	Right Ventricle	heart
11	chr6:74170600-74172600	Active TSS	Thymus	Thymus
12	chr6:74170600-74172600	Active TSS	HSMM	muscle
13	chr6:74170600-74172800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:74170600-74173000	Active TSS	Hela-S3	cervix
15	chr6:74170800-74171600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:74170800-74171600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:74170800-74171800	Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr6:74170800-74171800	Active TSS	Brain Substantia Nigra	brain
19	chr6:74170800-74172000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr6:74170800-74172000	Active TSS	Adipose Nuclei	Adipose
21	chr6:74170800-74172200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:74170800-74172200	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:74170800-74172200	Active TSS	Esophagus	oesophagus
24	chr6:74170800-74172200	Active TSS	Fetal Muscle Trunk	muscle
25	chr6:74170800-74172200	Active TSS	Lung	lung
26	chr6:74170800-74172200	Active TSS	Stomach Mucosa	stomach
27	chr6:74170800-74172400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:74170800-74172400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:74170800-74172400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr6:74170800-74172400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:74170800-74172400	Active TSS	Aorta	Aorta
32	chr6:74170800-74172400	Active TSS	Brain Cingulate Gyrus	brain
33	chr6:74170800-74172400	Active TSS	Fetal Intestine Small	intestine
34	chr6:74170800-74172400	Active TSS	Fetal Kidney	kidney
35	chr6:74170800-74172400	Active TSS	Left Ventricle	heart
36	chr6:74170800-74172600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:74170800-74172600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:74170800-74172600	Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:74170800-74172600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:74170800-74172600	Active TSS	Brain Angular Gyrus	brain
41	chr6:74170800-74172600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:74170800-74172600	Active TSS	Colonic Mucosa	Colon
43	chr6:74170800-74172600	Active TSS	Fetal Intestine Large	intestine
44	chr6:74170800-74172600	Active TSS	Fetal Lung	lung
45	chr6:74170800-74172600	Active TSS	Pancreas	Pancrea
46	chr6:74170800-74172600	Active TSS	Psoas Muscle	Psoas
47	chr6:74170800-74172600	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr6:74170800-74172600	Active TSS	Right Atrium	heart
49	chr6:74170800-74172600	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr6:74170800-74172600	Active TSS	HUVEC	blood vessel

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