Variant report

Variant	rs12198468
Chromosome Location	chr6:74171384-74171385
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:366)
CpG islands
(count:122)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

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	MTA3	chr6:74171341-74171966	GM12878	blood:	n/a	n/a
3	MXI1	chr6:74170750-74172266	SK-N-SH	brain:	n/a	n/a
4	REST	chr6:74171131-74172209	H1-neurons	neurons:	n/a	chr6:74171803-74171813
5	ZNF143	chr6:74171317-74172079	GM12878	blood:	n/a	n/a
6	FOXP2	chr6:74171362-74171675	SK-N-MC	brain:	n/a	n/a
7	YY1	chr6:74171290-74171906	NT2-D1	testis:	n/a	n/a
8	POLR2A	chr6:74171137-74171860	U87	brain:	n/a	n/a
9	CREB1	chr6:74171347-74171671	A549	lung:	n/a	n/a
10	GTF2F1	chr6:74170999-74172043	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr6:74171283-74171682	SK-N-SH	brain:	n/a	n/a
12	HCFC1	chr6:74171307-74172307	Hela-S3	cervix:	n/a	n/a
13	YY1	chr6:74171333-74172178	ECC-1	luminal epithelium:	n/a	n/a
14	ELF1	chr6:74171315-74171741	HepG2	liver:	n/a	n/a
15	CEBPB	chr6:74171377-74171649	K562	blood:	n/a	n/a
16	TAF1	chr6:74171326-74171976	GM12892	blood:	n/a	n/a
17	EP300	chr6:74170937-74171603	GM12878	blood:	n/a	n/a
18	EP300	chr6:74171166-74171561	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:74171261-74171954	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr6:74171314-74172094	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr6:74170778-74172020	HUVEC	blood vessel:	n/a	n/a
22	TAF1	chr6:74171303-74171974	MCF-7	breast:	n/a	n/a
23	CEBPB	chr6:74171331-74171903	MCF-7	breast:	n/a	n/a
24	TAF1	chr6:74171344-74171938	HepG2	liver:	n/a	n/a
25	NFYA	chr6:74171323-74171754	Hela-S3	cervix:	n/a	chr6:74171427-74171442 chr6:74171427-74171442 chr6:74171429-74171439
26	ZNF143	chr6:74171382-74171828	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr6:74171356-74171753	A549	lung:	n/a	n/a
28	NFYB	chr6:74171287-74172052	K562	blood:	n/a	chr6:74171424-74171439 chr6:74171427-74171442 chr6:74171427-74171442 chr6:74171429-74171439
29	GTF2F1	chr6:74171353-74171596	K562	blood:	n/a	n/a
30	JUND	chr6:74170675-74172132	GM12878	blood:	n/a	chr6:74171847-74171856 chr6:74171431-74171440
31	POLR2A	chr6:74171328-74171897	A549	lung:	n/a	n/a
32	ARID3A	chr6:74171335-74171775	HepG2	liver:	n/a	n/a
33	YY1	chr6:74171285-74172011	GM12878	blood:	n/a	n/a
34	CEBPB	chr6:74171325-74171965	A549	lung:	n/a	n/a
35	MAX	chr6:74171330-74172194	Hela-S3	cervix:	n/a	n/a
36	TAF1	chr6:74171320-74171938	PFSK-1	brain:	n/a	n/a
37	TBP	chr6:74171278-74171832	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:74171154-74171881	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr6:74171293-74171893	GM10847	blood:	n/a	n/a
40	IRF1	chr6:74171284-74171729	K562	blood:	n/a	n/a
41	POLR2A	chr6:74171311-74172049	GM12878	blood:	n/a	n/a
42	YY1	chr6:74171303-74171840	HepG2	liver:	n/a	n/a
43	STAT5A	chr6:74171299-74171989	GM12878	blood:	n/a	n/a
44	TCF7L2	chr6:74171333-74172105	Hela-S3	cervix:	n/a	n/a
45	CEBPD	chr6:74171340-74171640	HepG2	liver:	n/a	n/a
46	TAF1	chr6:74171261-74171971	SK-N-SH	brain:	n/a	n/a
47	USF1	chr6:74171364-74171571	SK-N-SH_RA	brain:	n/a	n/a
48	MAX	chr6:74171341-74171946	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr6:74171268-74172047	MCF10A-Er-Src	breast:	n/a	n/a
50	CEBPB	chr6:74171329-74171711	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:74171354-74171404	K562	blood:	n/a
2	chr6:74171354-74171404	HCT-116	colon:	n/a
3	chr6:74171350-74171400	GM12878	blood:	n/a
4	chr6:74171350-74171400	CMK	blood:	n/a
5	chr6:74171350-74171400	HMEC	breast:	n/a
6	chr6:74171354-74171404	GM12892	blood:	n/a
7	chr6:74171350-74171400	Hepatocyte	liver:	n/a
8	chr6:74171350-74171400	HRCEpiC	kidney:	n/a
9	chr6:74171354-74171404	HCF	heart:	n/a
10	chr6:74171350-74171400	AG09319	gingival:	n/a
11	chr6:74171350-74171400	H1-hESC	embryonic stem cell:	embryo
12	chr6:74171354-74171404	CMK	blood:	n/a
13	chr6:74171350-74171400	NT2-D1	testis:	n/a
14	chr6:74171354-74171404	PANC-1	pancreas:	n/a
15	chr6:74171350-74171400	MCF-7	breast:	n/a
16	chr6:74171350-74171400	A549	lung:	n/a
17	chr6:74171354-74171404	HEK293	kidney:	embryo
18	chr6:74171350-74171400	HRPEpiC	eye:	n/a
19	chr6:74171354-74171404	AoSMC	blood vessel:	n/a
20	chr6:74171354-74171404	AG09309	skin:	n/a
21	chr6:74171350-74171400	HL-60	blood:	n/a
22	chr6:74171350-74171400	HCPEpiC	choroid plexus:	n/a
23	chr6:74171354-74171404	ECC-1	luminal epithelium:	n/a
24	chr6:74171350-74171400	AoSMC	blood vessel:	n/a
25	chr6:74171354-74171404	NHBE	bronchial:	n/a
26	chr6:74171354-74171404	IMR90	lung:	fetal
27	chr6:74171350-74171400	Jurkat	blood:	n/a
28	chr6:74171350-74171400	AG09309	skin:	n/a
29	chr6:74171350-74171400	SAEC	small airway:	n/a
30	chr6:74171350-74171400	PrEC	prostate:	n/a
31	chr6:74171354-74171404	AG04450	lung:	fetal
32	chr6:74171354-74171404	U87	brain:	n/a
33	chr6:74171354-74171404	BJ	skin:	n/a
34	chr6:74171350-74171400	NB4	blood:	n/a
35	chr6:74171350-74171400	HNPCEpiC	eye:	n/a
36	chr6:74171354-74171404	Hepatocyte	liver:	n/a
37	chr6:74171354-74171404	HNPCEpiC	eye:	n/a
38	chr6:74171354-74171404	MCF10A-Er-Src	breast:	n/a
39	chr6:74171354-74171404	SK-N-SH	brain:	n/a
40	chr6:74171354-74171404	NB4	blood:	n/a
41	chr6:74171350-74171400	SK-N-SH_RA	brain:	n/a
42	chr6:74171354-74171404	T-47D	breast:	n/a
43	chr6:74171350-74171400	RPTEC	kidney:	n/a
44	chr6:74171350-74171400	GM12891	blood:	n/a
45	chr6:74171354-74171404	HIPEpiC	eye:	n/a
46	chr6:74171350-74171400	NHBE	bronchial:	n/a
47	chr6:74171350-74171400	HEK293	kidney:	embryo
48	chr6:74171354-74171404	AG10803	skin:	n/a
49	chr6:74171350-74171400	Hela-S3	cervix:	n/a
50	chr6:74171354-74171404	NHDF-neo	bronchial:	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
RNU6-975P	CpG island
MTO1	CpG island
ENSG00000203907	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000234882	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000224221	Chromatin interaction

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

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

rs_ID	r²[population]
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]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12198468	MTO1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74170400-74171400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:74170400-74172400	Active TSS	Dnd41	blood
3	chr6:74170600-74171600	Active TSS	Stomach Smooth Muscle	stomach
4	chr6:74170600-74172200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:74170600-74172400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:74170600-74172400	Active TSS	Brain Germinal Matrix	brain
7	chr6:74170600-74172400	Active TSS	Fetal Stomach	stomach
8	chr6:74170600-74172600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr6:74170600-74172600	Active TSS	Primary T cells from cord blood	blood
10	chr6:74170600-74172600	Active TSS	Duodenum Mucosa	Duodenum
11	chr6:74170600-74172600	Active TSS	Right Ventricle	heart
12	chr6:74170600-74172600	Active TSS	Thymus	Thymus
13	chr6:74170600-74172600	Active TSS	HSMM	muscle
14	chr6:74170600-74172800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:74170600-74173000	Active TSS	Hela-S3	cervix
16	chr6:74170800-74171600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:74170800-74171600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:74170800-74171800	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr6:74170800-74171800	Active TSS	Brain Substantia Nigra	brain
20	chr6:74170800-74172000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:74170800-74172000	Active TSS	Adipose Nuclei	Adipose
22	chr6:74170800-74172200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:74170800-74172200	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr6:74170800-74172200	Active TSS	Esophagus	oesophagus
25	chr6:74170800-74172200	Active TSS	Fetal Muscle Trunk	muscle
26	chr6:74170800-74172200	Active TSS	Lung	lung
27	chr6:74170800-74172200	Active TSS	Stomach Mucosa	stomach
28	chr6:74170800-74172400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:74170800-74172400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:74170800-74172400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr6:74170800-74172400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:74170800-74172400	Active TSS	Aorta	Aorta
33	chr6:74170800-74172400	Active TSS	Brain Cingulate Gyrus	brain
34	chr6:74170800-74172400	Active TSS	Fetal Intestine Small	intestine
35	chr6:74170800-74172400	Active TSS	Fetal Kidney	kidney
36	chr6:74170800-74172400	Active TSS	Left Ventricle	heart
37	chr6:74170800-74172600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:74170800-74172600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:74170800-74172600	Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:74170800-74172600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:74170800-74172600	Active TSS	Brain Angular Gyrus	brain
42	chr6:74170800-74172600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:74170800-74172600	Active TSS	Colonic Mucosa	Colon
44	chr6:74170800-74172600	Active TSS	Fetal Intestine Large	intestine
45	chr6:74170800-74172600	Active TSS	Fetal Lung	lung
46	chr6:74170800-74172600	Active TSS	Pancreas	Pancrea
47	chr6:74170800-74172600	Active TSS	Psoas Muscle	Psoas
48	chr6:74170800-74172600	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr6:74170800-74172600	Active TSS	Right Atrium	heart
50	chr6:74170800-74172600	Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links