Variant report

Variant	rs6490265
Chromosome Location	chr12:120105707-120105708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:544)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:544 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120105570-120106052	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr12:120105497-120105836	HUVEC	blood vessel:	n/a	n/a
3	MAFK	chr12:120105630-120105986	HepG2	liver:	n/a	chr12:120105882-120105891
4	POLR2A	chr12:120105556-120106452	K562	blood:	n/a	n/a
5	MYC	chr12:120105426-120105957	MCF10A-Er-Src	breast:	n/a	n/a
6	TAF1	chr12:120105534-120105992	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:120105479-120106072	A549	lung:	n/a	n/a
8	CTCF	chr12:120105700-120105850	AG10803	skin:	n/a	n/a
9	CTCF	chr12:120105700-120105850	AG09309	skin:	n/a	n/a
10	GABPA	chr12:120105307-120106371	MCF-7	breast:	n/a	chr12:120105759-120105766 chr12:120105598-120105612 chr12:120105669-120105676
11	YY1	chr12:120105135-120106136	SK-N-SH_RA	brain:	n/a	chr12:120105230-120105240 chr12:120105708-120105717
12	E2F4	chr12:120105603-120105906	GM12878	blood:	n/a	n/a
13	MAX	chr12:120105185-120106252	NB4	blood:	n/a	n/a
14	MAX	chr12:120105156-120106251	MCF-7	breast:	n/a	n/a
15	SRF	chr12:120105609-120105917	K562	blood:	n/a	n/a
16	NFIC	chr12:120104029-120105869	GM12878	blood:	n/a	n/a
17	NFIC	chr12:120105445-120106015	GM12878	blood:	n/a	n/a
18	GABPA	chr12:120105391-120106154	Hela-S3	cervix:	n/a	chr12:120105759-120105766 chr12:120105598-120105612 chr12:120105669-120105676
19	BRCA1	chr12:120105519-120105866	GM12878	blood:	n/a	n/a
20	MAX	chr12:120105079-120106179	ECC-1	luminal epithelium:	n/a	n/a
21	STAT3	chr12:120105604-120105888	MCF10A-Er-Src	breast:	n/a	n/a
22	SMC3	chr12:120105337-120106196	Hela-S3	cervix:	n/a	chr12:120105536-120105546 chr12:120105536-120105550
23	TCF12	chr12:120105406-120105985	GM12878	blood:	n/a	n/a
24	MAFK	chr12:120105301-120106069	K562	blood:	n/a	chr12:120105882-120105891
25	POLR2A	chr12:120105498-120106332	PANC-1	pancreas:	n/a	n/a
26	NFIC	chr12:120105603-120105928	HepG2	liver:	n/a	n/a
27	SIN3AK20	chr12:120105626-120105908	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:120105582-120106084	H1-hESC	embryonic stem cell:	n/a	n/a
29	SMARCB1	chr12:120105430-120106315	Hela-S3	cervix:	n/a	n/a
30	ELF1	chr12:120105388-120106155	HepG2	liver:	n/a	chr12:120105754-120105763 chr12:120105759-120105768
31	JUND	chr12:120105361-120105987	A549	lung:	n/a	n/a
32	MYC	chr12:120105653-120105898	HepG2	liver:	n/a	n/a
33	TAF1	chr12:120105562-120106075	Hela-S3	cervix:	n/a	n/a
34	THAP1	chr12:120105479-120105997	K562	blood:	n/a	n/a
35	TBP	chr12:120105440-120106325	H1-hESC	embryonic stem cell:	n/a	n/a
36	E2F6	chr12:120105521-120105977	A549	lung:	n/a	n/a
37	MAX	chr12:120105167-120106208	HCT-116	colon:	n/a	n/a
38	YY1	chr12:120105160-120106231	GM12878	blood:	n/a	chr12:120105230-120105240 chr12:120105708-120105717
39	TAF7	chr12:120105586-120106042	H1-hESC	embryonic stem cell:	n/a	n/a
40	HEY1	chr12:120105572-120106124	HepG2	liver:	n/a	n/a
41	POLR2A	chr12:120105497-120106140	ProgFib	skin:	n/a	n/a
42	STAT5A	chr12:120105648-120106013	GM12878	blood:	n/a	n/a
43	SIN3AK20	chr12:120105581-120106221	H1-hESC	embryonic stem cell:	n/a	n/a
44	SP1	chr12:120105428-120105962	GM12878	blood:	n/a	chr12:120105914-120105924 chr12:120105915-120105924 chr12:120105914-120105924
45	POLR2A	chr12:120105388-120106189	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr12:120105439-120106350	HL-60	blood:	n/a	n/a
47	IRF1	chr12:120105281-120106013	K562	blood:	n/a	chr12:120105666-120105686
48	TAL1	chr12:120105366-120106031	K562	blood:	n/a	n/a
49	REST	chr12:120104955-120106284	H1-neurons	neurons:	n/a	chr12:120105588-120105598
50	CTCF	chr12:120105403-120105713	A549	lung:	n/a	chr12:120105536-120105549 chr12:120105534-120105552 chr12:120105535-120105551

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:120105695-120105745	GM19239	blood:	n/a
2	chr12:120105695-120105745	SK-N-MC	brain:	n/a
3	chr12:120105695-120105745	LNCaP	prostate:	n/a
4	chr12:120105695-120105745	SAEC	small airway:	n/a
5	chr12:120105695-120105745	U87	brain:	n/a
6	chr12:120105695-120105745	NT2-D1	testis:	n/a
7	chr12:120105695-120105745	AG10803	skin:	n/a
8	chr12:120105695-120105745	HNPCEpiC	eye:	n/a
9	chr12:120105695-120105745	H1-hESC	embryonic stem cell:	embryo
10	chr12:120105695-120105745	NH-A	brain:	n/a
11	chr12:120105695-120105745	HRPEpiC	eye:	n/a
12	chr12:120105695-120105745	HMEC	breast:	n/a
13	chr12:120105695-120105745	HUVEC	blood vessel:	n/a
14	chr12:120105695-120105745	HIPEpiC	eye:	n/a
15	chr12:120105695-120105745	HL-60	blood:	n/a
16	chr12:120105695-120105745	PANC-1	pancreas:	n/a
17	chr12:120105695-120105745	AG09319	gingival:	n/a
18	chr12:120105695-120105745	HEEpiC	esophagus:	n/a
19	chr12:120105695-120105745	BE2_C	brain:	n/a
20	chr12:120105695-120105745	Jurkat	blood:	n/a
21	chr12:120105695-120105745	HCT-116	colon:	n/a
22	chr12:120105695-120105745	AG09309	skin:	n/a
23	chr12:120105695-120105745	HCF	heart:	n/a
24	chr12:120105695-120105745	AG04449	skin:	fetal
25	chr12:120105695-120105745	CMK	blood:	n/a
26	chr12:120105695-120105745	GM12878	blood:	n/a
27	chr12:120105695-120105745	HEK293	kidney:	embryo
28	chr12:120105695-120105745	K562	blood:	n/a
29	chr12:120105695-120105745	HPAEpiC	pulmonary alveolar:	n/a
30	chr12:120105695-120105745	ECC-1	luminal epithelium:	n/a
31	chr12:120105695-120105745	HRE	kidney:	n/a
32	chr12:120105695-120105745	Hela-S3	cervix:	n/a
33	chr12:120105695-120105745	AG04450	lung:	fetal
34	chr12:120105695-120105745	MCF-7	breast:	n/a
35	chr12:120105695-120105745	HCPEpiC	choroid plexus:	n/a
36	chr12:120105695-120105745	GM06990	blood:	n/a
37	chr12:120105695-120105745	A549	lung:	n/a
38	chr12:120105695-120105745	PrEC	prostate:	n/a
39	chr12:120105695-120105745	SK-N-SH	brain:	n/a
40	chr12:120105695-120105745	Hepatocyte	liver:	n/a
41	chr12:120105695-120105745	HRCEpiC	kidney:	n/a
42	chr12:120105695-120105745	RPTEC	kidney:	n/a
43	chr12:120105695-120105745	ProgFib	skin:	n/a
44	chr12:120105695-120105745	MCF10A-Er-Src	breast:	n/a
45	chr12:120105695-120105745	NB4	blood:	n/a
46	chr12:120105695-120105745	SKMC	muscle:	n/a
47	chr12:120105695-120105745	GM12891	blood:	n/a
48	chr12:120105695-120105745	SK-N-SH_RA	brain:	n/a
49	chr12:120105695-120105745	BJ	skin:	n/a
50	chr12:120105695-120105745	ovcar-3	ovarian:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120105637..120106241-chr17:79303862..79304549,2	Hela-S3	cervix:
2	chr12:120104659..120106467-chr4:174254824..174256542,2	MCF-7	breast:
3	chr12:120105362..120106356-chr3:119813905..119814759,2	NB4	blood:
4	chr12:120104750..120107660-chr12:120111377..120114502,3	MCF-7	breast:
5	chr12:120104335..120107623-chr12:120110345..120114528,7	MCF-7	breast:
6	chr12:118812486..118814761-chr12:120105257..120106996,2	K562	blood:
7	chr12:120105122..120114412-chr12:120115205..120125435,13	MCF-7	breast:
8	chr12:120104565..120106668-chr12:120729361..120730960,2	K562	blood:
9	chr12:120105026..120107337-chr12:120115955..120117891,2	MCF-7	breast:
10	chr12:120105686..120108054-chr12:120134136..120136155,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRKAB1	TF binding region
PRKAB1	CpG island
ENSG00000270482	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000111725	Chromatin interaction
ENSG00000185332	Chromatin interaction
ENSG00000164104	Chromatin interaction
ENSG00000122966	Chromatin interaction
ENSG00000242622	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10774512	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10849687	0.89[ASN][1000 genomes]
rs11064868	0.87[ASN][1000 genomes]
rs11064874	0.89[ASN][1000 genomes]
rs12309592	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1318272	0.81[JPT][hapmap]
rs175879	0.81[JPT][hapmap]
rs1966324	0.84[ASN][1000 genomes]
rs1985793	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs202985	0.82[JPT][hapmap]
rs2393549	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2393550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278124	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs278128	0.81[JPT][hapmap]
rs278129	0.81[JPT][hapmap]
rs278130	0.81[JPT][hapmap]
rs278131	0.81[JPT][hapmap]
rs278135	0.82[JPT][hapmap]
rs2893806	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3213626	0.82[JPT][hapmap]
rs4766946	0.82[JPT][hapmap]
rs4767838	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6490262	0.85[ASN][1000 genomes]
rs6490263	0.86[ASN][1000 genomes]
rs6490264	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7953776	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7969977	0.90[ASN][1000 genomes]
rs904654	0.86[JPT][hapmap]
rs904655	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120104800-120105800	Active TSS	Primary T cells fromperipheralblood	blood
2	chr12:120104800-120105800	Enhancers	Stomach Mucosa	stomach
3	chr12:120104800-120106000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:120104800-120106200	Active TSS	Brain Cingulate Gyrus	brain
5	chr12:120104800-120106400	Active TSS	Fetal Thymus	thymus
6	chr12:120104800-120106800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:120104800-120106800	Active TSS	Right Ventricle	heart
8	chr12:120104800-120106800	Active TSS	Stomach Smooth Muscle	stomach
9	chr12:120104800-120107800	Active TSS	Rectal Smooth Muscle	rectum
10	chr12:120105000-120105800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:120105000-120105800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:120105000-120105800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:120105000-120106200	Active TSS	Thymus	Thymus
14	chr12:120105000-120106600	Active TSS	Fetal Muscle Trunk	muscle
15	chr12:120105000-120106600	Active TSS	Right Atrium	heart
16	chr12:120105000-120106800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:120105000-120106800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr12:120105000-120106800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:120105000-120106800	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:120105000-120106800	Active TSS	Brain Anterior Caudate	brain
21	chr12:120105000-120106800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:120105000-120106800	Active TSS	HSMMtube	muscle
23	chr12:120105000-120106800	Active TSS	NHDF-Ad	bronchial
24	chr12:120105000-120107000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr12:120105000-120107000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:120105000-120107000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:120105000-120107000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:120105000-120107400	Active TSS	Colonic Mucosa	Colon
29	chr12:120105200-120105800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:120105200-120105800	Active TSS	Brain Germinal Matrix	brain
31	chr12:120105200-120105800	Active TSS	HepG2	liver
32	chr12:120105200-120106000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:120105200-120106200	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr12:120105200-120106200	Active TSS	Spleen	Spleen
35	chr12:120105200-120106400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:120105200-120106400	Active TSS	Brain Angular Gyrus	brain
37	chr12:120105200-120106400	Active TSS	Ovary	ovary
38	chr12:120105200-120106600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:120105200-120106600	Active TSS	Aorta	Aorta
40	chr12:120105200-120106600	Active TSS	Left Ventricle	heart
41	chr12:120105200-120106600	Active TSS	Lung	lung
42	chr12:120105200-120106600	Active TSS	Placenta Amnion	Placenta Amnion
43	chr12:120105200-120106800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:120105200-120106800	Active TSS	H9 Cell Line	embryonic stem cell
45	chr12:120105200-120106800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:120105200-120106800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr12:120105200-120106800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:120105200-120106800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:120105200-120106800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:120105200-120106800	Active TSS	Brain Substantia Nigra	brain

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