Variant report

Variant	rs1466512
Chromosome Location	chr12:56223613-56223614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:492)
CpG islands
(count:61)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:492 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr12:56223155-56223829	A549	lung:	n/a	n/a
2	GABPA	chr12:56223216-56223694	HepG2	liver:	n/a	n/a
3	STAT1	chr12:56223268-56223722	GM12878	blood:	n/a	chr12:56223316-56223328
4	POLR2A	chr12:56223120-56224751	HEK293	kidney:	n/a	n/a
5	GABPA	chr12:56223207-56223995	SK-N-SH	brain:	n/a	n/a
6	ZNF143	chr12:56223273-56223768	Hela-S3	cervix:	n/a	n/a
7	MYC	chr12:56223352-56223697	MCF-7	breast:	n/a	n/a
8	POLR2A	chr12:56223161-56223811	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr12:56223253-56223681	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:56222883-56224839	GM18505	blood:	n/a	n/a
11	POLR2A	chr12:56223209-56225353	H1-neurons	neurons:	n/a	n/a
12	SP2	chr12:56223221-56223617	H1-hESC	embryonic stem cell:	n/a	chr12:56223466-56223489
13	POLR2A	chr12:56223086-56224836	Raji	blood:	n/a	n/a
14	TAF1	chr12:56223267-56223719	A549	lung:	n/a	n/a
15	CHD2	chr12:56223260-56223787	HepG2	liver:	n/a	n/a
16	FOS	chr12:56223312-56223641	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:56223074-56223857	GM12878	blood:	n/a	n/a
18	FOXA1	chr12:56223237-56223683	T-47D	breast:	n/a	n/a
19	GABPA	chr12:56223230-56223846	GM12878	blood:	n/a	n/a
20	ZMIZ1	chr12:56223221-56223690	K562	blood:	n/a	n/a
21	HNF4A	chr12:56223321-56223943	HepG2	liver:	n/a	chr12:56223613-56223628 chr12:56223613-56223628 chr12:56223613-56223628 chr12:56223613-56223628 chr12:56223615-56223627 chr12:56223613-56223628 chr12:56223613-56223628 chr12:56223615-56223627 chr12:56223614-56223627 chr12:56223421-56223437
22	SIN3AK20	chr12:56223232-56223697	PFSK-1	brain:	n/a	n/a
23	MYC	chr12:56223258-56223738	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr12:56222948-56223985	U87	brain:	n/a	n/a
25	CREB1	chr12:56223156-56223756	A549	lung:	n/a	n/a
26	SP1	chr12:56223136-56225011	HCT-116	colon:	n/a	chr12:56223349-56223363 chr12:56223348-56223360
27	CREB1	chr12:56223197-56223666	A549	lung:	n/a	n/a
28	PBX3	chr12:56223201-56223843	SK-N-SH	brain:	n/a	chr12:56223467-56223487
29	POLR2A	chr12:56222695-56224993	ECC-1	luminal epithelium:	n/a	n/a
30	SIN3A	chr12:56223218-56225194	H1-hESC	embryonic stem cell:	n/a	chr12:56223337-56223350
31	NANOG	chr12:56223349-56223684	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr12:56223189-56223729	A549	lung:	n/a	chr12:56223387-56223398 chr12:56223348-56223362 chr12:56223387-56223396 chr12:56223388-56223402
33	POLR2A	chr12:56223104-56224219	GM19099	blood:	n/a	n/a
34	POLR2A	chr12:56222788-56225023	HepG2	liver:	n/a	n/a
35	MXI1	chr12:56223255-56223794	K562	blood:	n/a	n/a
36	NFIC	chr12:56223167-56224740	ECC-1	luminal epithelium:	n/a	n/a
37	YY1	chr12:56223187-56223797	SK-N-SH	brain:	n/a	chr12:56223387-56223398 chr12:56223348-56223362 chr12:56223387-56223396 chr12:56223388-56223402
38	NR2C2	chr12:56223230-56223631	K562	blood:	n/a	chr12:56223423-56223430
39	REST	chr12:56223189-56223838	HL-60	blood:	n/a	chr12:56223337-56223350 chr12:56223340-56223353 chr12:56223316-56223329
40	MAZ	chr12:56222508-56225685	IMR90	lung:	n/a	chr12:56225419-56225428
41	POLR2A	chr12:56222943-56224986	MCF-7	breast:	n/a	n/a
42	ELF1	chr12:56223193-56224330	MCF-7	breast:	n/a	chr12:56223420-56223429 chr12:56223389-56223401 chr12:56223343-56223355 chr12:56223419-56223430 chr12:56223419-56223430
43	ELF1	chr12:56222705-56224939	GM12878	blood:	n/a	chr12:56223420-56223429 chr12:56223389-56223401 chr12:56223343-56223355 chr12:56224404-56224417 chr12:56223419-56223430 chr12:56223419-56223430
44	POLR2A	chr12:56223010-56224283	MCF-7	breast:	n/a	n/a
45	E2F6	chr12:56223229-56223683	K562	blood:	n/a	n/a
46	JUND	chr12:56223254-56224849	K562	blood:	n/a	n/a
47	TEAD4	chr12:56223261-56224326	HepG2	liver:	n/a	n/a
48	POLR2A	chr12:56223177-56224366	HL-60	blood:	n/a	n/a
49	E2F4	chr12:56223273-56224251	K562	blood:	n/a	n/a
50	EGR1	chr12:56223194-56224250	K562	blood:	n/a	chr12:56223867-56223881 chr12:56223914-56223928 chr12:56223419-56223428

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56223597-56223647	IMR90	lung:	fetal
2	chr12:56223597-56223647	NHDF-neo	bronchial:	n/a
3	chr12:56223597-56223647	BE2_C	brain:	n/a
4	chr12:56223597-56223647	PANC-1	pancreas:	n/a
5	chr12:56223597-56223647	U87	brain:	n/a
6	chr12:56223597-56223647	HRCEpiC	kidney:	n/a
7	chr12:56223597-56223647	Jurkat	blood:	n/a
8	chr12:56223597-56223647	HCF	heart:	n/a
9	chr12:56223597-56223647	MCF10A-Er-Src	breast:	n/a
10	chr12:56223597-56223647	A549	lung:	n/a
11	chr12:56223597-56223647	AoSMC	blood vessel:	n/a
12	chr12:56223597-56223647	SK-N-SH_RA	brain:	n/a
13	chr12:56223597-56223647	GM12891	blood:	n/a
14	chr12:56223597-56223647	Hela-S3	cervix:	n/a
15	chr12:56223597-56223647	AG10803	skin:	n/a
16	chr12:56223597-56223647	NH-A	brain:	n/a
17	chr12:56223597-56223647	CMK	blood:	n/a
18	chr12:56223597-56223647	AG04449	skin:	fetal
19	chr12:56223597-56223647	ECC-1	luminal epithelium:	n/a
20	chr12:56223597-56223647	SAEC	small airway:	n/a
21	chr12:56223597-56223647	T-47D	breast:	n/a
22	chr12:56223597-56223647	HRE	kidney:	n/a
23	chr12:56223597-56223647	AG04450	lung:	fetal
24	chr12:56223597-56223647	HEK293	kidney:	embryo
25	chr12:56223597-56223647	K562	blood:	n/a
26	chr12:56223597-56223647	SK-N-SH	brain:	n/a
27	chr12:56223597-56223647	AG09309	skin:	n/a
28	chr12:56223597-56223647	HCPEpiC	choroid plexus:	n/a
29	chr12:56223597-56223647	H1-hESC	embryonic stem cell:	embryo
30	chr12:56223597-56223647	NB4	blood:	n/a
31	chr12:56223597-56223647	HCT-116	colon:	n/a
32	chr12:56223597-56223647	Caco-2	colon:	n/a
33	chr12:56223597-56223647	ovcar-3	ovarian:	n/a
34	chr12:56223597-56223647	NT2-D1	testis:	n/a
35	chr12:56223597-56223647	MCF-7	breast:	n/a
36	chr12:56223597-56223647	SK-N-MC	brain:	n/a
37	chr12:56223597-56223647	HIPEpiC	eye:	n/a
38	chr12:56223597-56223647	GM19239	blood:	n/a
39	chr12:56223597-56223647	HCM	heart:	n/a
40	chr12:56223597-56223647	HNPCEpiC	eye:	n/a
41	chr12:56223597-56223647	HRPEpiC	eye:	n/a
42	chr12:56223597-56223647	Hepatocyte	liver:	n/a
43	chr12:56223597-56223647	GM12878	blood:	n/a
44	chr12:56223597-56223647	HepG2	liver:	n/a
45	chr12:56223597-56223647	RPTEC	kidney:	n/a
46	chr12:56223597-56223647	HAEpiC	amniotic membrane:	n/a
47	chr12:56223597-56223647	PFSK-1	brain:	n/a
48	chr12:56223597-56223647	GM12892	blood:	n/a
49	chr12:56223597-56223647	BJ	skin:	n/a
50	chr12:56223597-56223647	ProgFib	skin:	n/a

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56222205..56224922-chr12:56358822..56360561,2	MCF-7	breast:
2	chr12:56222874..56225459-chr12:56331362..56334369,4	MCF-7	breast:
3	chr12:56222506..56227501-chr12:56233677..56237355,4	K562	blood:
4	chr12:56222034..56224424-chr12:56351051..56353709,2	MCF-7	breast:
5	chr12:56222083..56225232-chr12:56434095..56438071,8	MCF-7	breast:
6	chr12:56222395..56225334-chr12:56325812..56327785,2	K562	blood:
7	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
8	chr12:56217816..56225905-chr12:56319649..56327312,13	K562	blood:
9	chr12:56223374..56223959-chr6:99968442..99968978,2	HCT-116	colon:
10	chr12:53454054..53456041-chr12:56223031..56224851,2	MCF-7	breast:
11	chr12:56222158..56225126-chr12:56264832..56267063,2	MCF-7	breast:
12	chr12:56223208..56223963-chr13:60970516..60971430,2	NB4	blood:
13	chr12:56223504..56226231-chr17:81007851..81010191,2	MCF-7	breast:
14	chr12:56221380..56224964-chr12:56389518..56391626,4	MCF-7	breast:
15	chr12:56223221..56225412-chr12:56473813..56476164,2	MCF-7	breast:
16	chr12:56223378..56224108-chrX:16737584..16738175,2	Hela-S3	cervix:
17	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
18	chr12:56219783..56227072-chr12:56318292..56323886,14	K562	blood:
19	chr12:56223309..56224865-chr12:56552081..56554400,2	MCF-7	breast:
20	chr12:56221995..56224652-chr12:56472013..56474310,2	MCF-7	breast:
21	chr12:56222536..56225150-chr12:56365763..56368658,3	MCF-7	breast:
22	chr12:56222339..56223963-chr12:56389750..56392232,2	MCF-7	breast:
23	chr12:56222623..56225394-chr12:56346640..56348578,2	K562	blood:
24	chr12:56222332..56225809-chr12:56227507..56233140,8	K562	blood:
25	chr12:56221810..56225034-chr12:56267373..56269273,5	MCF-7	breast:
26	chr12:56223489..56225123-chr12:120729233..120730868,2	MCF-7	breast:
27	chr12:56222612..56225517-chr12:56372520..56376647,5	MCF-7	breast:
28	chr12:56221098..56224816-chr12:56434415..56439287,4	MCF-7	breast:
29	chr12:56223245..56223790-chr19:9929001..9929774,2	NB4	blood:
30	chr12:56217492..56232243-chr12:56318854..56330686,48	MCF-7	breast:
31	chr12:56221925..56223958-chr8:101962286..101964475,2	MCF-7	breast:
32	chr12:56223515..56224135-chr22:43011020..43011910,2	Hela-S3	cervix:
33	chr12:56223239..56223746-chr12:56320304..56321029,2	MCF-7	breast:
34	chr12:56223409..56227527-chr12:56348845..56352516,3	MCF-7	breast:
35	chr12:56222629..56224210-chr12:56360476..56363033,2	MCF-7	breast:
36	chr12:56222087..56223926-chr12:56400815..56402785,2	MCF-7	breast:
37	chr12:56220285..56224153-chr12:56233677..56238372,4	K562	blood:

No data

Variant related genes	Relation type
DNAJC14	TF binding region
TMEM198B	TF binding region
ENSG00000257390	TF binding region
ENSG00000257390	CpG island
TMEM198B	CpG island
DNAJC14	CpG island
ENSG00000207339	Chromatin interaction
ENSG00000169895	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000111077	Chromatin interaction
ENSG00000083544	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000228439	Chromatin interaction
ENSG00000175711	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000257966	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000123342	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000127452	Chromatin interaction
ENSG00000111540	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1681085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689516	1.00[MEX][hapmap]
rs1701705	1.00[MEX][hapmap]
rs1725358	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1871999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449476	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2462938	1.00[AMR][1000 genomes]
rs2694008	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2694015	1.00[AMR][1000 genomes]
rs2887997	1.00[AMR][1000 genomes]
rs4759012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4759202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55884432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7305623	1.00[MEX][hapmap]
rs7310325	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772250	1.00[AMR][1000 genomes]
rs772251	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs772252	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772253	1.00[AMR][1000 genomes]
rs772256	1.00[AMR][1000 genomes]
rs772257	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs772259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772261	1.00[AMR][1000 genomes]
rs7956337	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs7963379	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs808896	1.00[MEX][hapmap]
rs812230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 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	chr12:56220000-56225400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:56222200-56224400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:56222200-56225000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:56222400-56224000	Active TSS	HMEC	breast
5	chr12:56222400-56224400	Active TSS	Colonic Mucosa	Colon
6	chr12:56222400-56224800	Active TSS	NHLF	lung
7	chr12:56222400-56225000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:56222400-56225000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr12:56222400-56225000	Active TSS	Right Ventricle	heart
10	chr12:56222400-56225400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:56222400-56225600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:56222400-56225600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:56222600-56224000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:56222600-56224000	Active TSS	NH-A	brain
15	chr12:56222600-56224600	Active TSS	K562	blood
16	chr12:56222600-56224800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:56222600-56224800	Active TSS	Lung	lung
18	chr12:56222600-56224800	Active TSS	GM12878-XiMat	blood
19	chr12:56222600-56224800	Active TSS	HSMM	muscle
20	chr12:56222600-56225000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr12:56222600-56225000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:56222600-56225000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:56222600-56225000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:56222600-56225000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:56222600-56225000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:56222600-56225000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:56222600-56225000	Active TSS	Brain Anterior Caudate	brain
28	chr12:56222600-56225000	Active TSS	Esophagus	oesophagus
29	chr12:56222600-56225000	Active TSS	Fetal Intestine Small	intestine
30	chr12:56222600-56225000	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr12:56222600-56225200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:56222600-56225200	Active TSS	Brain Angular Gyrus	brain
33	chr12:56222600-56225200	Active TSS	Left Ventricle	heart
34	chr12:56222600-56225400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr12:56222600-56225400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr12:56222600-56225400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:56222600-56225400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr12:56222600-56225400	Active TSS	HSMMtube	muscle
39	chr12:56222600-56225600	Active TSS	Fetal Kidney	kidney
40	chr12:56222600-56225600	Active TSS	NHDF-Ad	bronchial
41	chr12:56222600-56226000	Active TSS	Rectal Smooth Muscle	rectum
42	chr12:56222800-56223800	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr12:56222800-56223800	Active TSS	Stomach Smooth Muscle	stomach
44	chr12:56222800-56224200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:56222800-56224200	Active TSS	Hela-S3	cervix
46	chr12:56222800-56224200	Active TSS	NHEK	skin
47	chr12:56222800-56224400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:56222800-56224400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr12:56222800-56224400	Active TSS	Osteobl	bone
50	chr12:56222800-56224600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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