Variant report

Variant	rs73336393
Chromosome Location	chr12:56334258-56334259
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:317)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:317 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:56334073-56334368	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr12:56333761-56334558	HCT-116	colon:	n/a	n/a
3	CTCF	chr12:56334067-56334329	LNCaP	prostate:	n/a	n/a
4	CTCF	chr12:56333986-56334338	A549	lung:	n/a	n/a
5	CTCF	chr12:56333791-56334549	MCF-7	breast:	n/a	n/a
6	RAD21	chr12:56333926-56334404	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr12:56333921-56334370	A549	lung:	n/a	n/a
8	JUND	chr12:56334078-56334273	HepG2	liver:	n/a	n/a
9	CTCF	chr12:56334140-56334290	HAc	cerebellar:	n/a	n/a
10	RAD21	chr12:56333923-56334476	H1-hESC	embryonic stem cell:	n/a	n/a
11	BCLAF1	chr12:56333924-56334471	GM12878	blood:	n/a	n/a
12	CTCF	chr12:56334140-56334290	GM12875	blood:	n/a	n/a
13	CTCF	chr12:56334160-56334310	HEK293	kidney:	n/a	n/a
14	CTCF	chr12:56334043-56334402	GM12892	blood:	n/a	n/a
15	CTCF	chr12:56334140-56334290	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr12:56334160-56334310	HPF	lung:	n/a	n/a
17	CTCF	chr12:56334074-56334335	Kidney_OC	kidney:	n/a	n/a
18	CTCF	chr12:56334180-56334330	HVMF	connective:	n/a	n/a
19	CTCF	chr12:56334120-56334270	HA-sp	spinal cord:	n/a	n/a
20	CTCF	chr12:56334087-56334358	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr12:56334160-56334310	GM12871	blood:	n/a	n/a
22	CTCF	chr12:56334067-56334359	K562	blood:	n/a	n/a
23	CTCF	chr12:56334180-56334330	HFF-Myc	foreskin:	n/a	n/a
24	RUNX3	chr12:56333765-56334419	GM12878	blood:	n/a	n/a
25	TCF12	chr12:56333805-56334467	A549	lung:	n/a	n/a
26	RAD21	chr12:56334010-56334389	HepG2	liver:	n/a	n/a
27	YY1	chr12:56334001-56334396	GM12892	blood:	n/a	n/a
28	MAZ	chr12:56334002-56334319	GM12878	blood:	n/a	chr12:56334035-56334045
29	CTCF	chr12:56334102-56334349	GM13976	blood:	n/a	n/a
30	CTCF	chr12:56334075-56334350	HepG2	liver:	n/a	n/a
31	CTCF	chr12:56334140-56334290	WERI-Rb-1	eye:	n/a	n/a
32	MTA3	chr12:56333935-56334626	GM12878	blood:	n/a	n/a
33	CTCF	chr12:56334120-56334270	GM12872	blood:	n/a	n/a
34	CTCF	chr12:56334033-56334365	A549	lung:	n/a	n/a
35	STAT1	chr12:56334040-56334385	GM12878	blood:	n/a	n/a
36	ZNF143	chr12:56334037-56334378	GM12878	blood:	n/a	n/a
37	MAX	chr12:56333978-56334268	K562	blood:	n/a	chr12:56334035-56334045
38	MAX	chr12:56333846-56334485	K562	blood:	n/a	chr12:56334035-56334045
39	ATF3	chr12:56333908-56334428	A549	lung:	n/a	n/a
40	CTCF	chr12:56334039-56334386	GM19238	blood:	n/a	n/a
41	EP300	chr12:56334021-56334295	GM12878	blood:	n/a	n/a
42	ZNF143	chr12:56334011-56334375	H1-hESC	embryonic stem cell:	n/a	n/a
43	USF2	chr12:56333957-56334323	Hela-S3	cervix:	n/a	n/a
44	FOXM1	chr12:56333921-56334450	GM12878	blood:	n/a	n/a
45	CTCF	chr12:56334140-56334290	GM12871	blood:	n/a	n/a
46	CTCF	chr12:56334120-56334270	NHEK	skin:	n/a	n/a
47	BHLHE40	chr12:56334050-56334379	K562	blood:	n/a	n/a
48	CTCF	chr12:56333965-56334394	HepG2	liver:	n/a	n/a
49	MYC	chr12:56334063-56334357	H1-hESC	embryonic stem cell:	n/a	n/a
50	TCF7L2	chr12:56334030-56334270	PANC-1	pancreas:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56334110..56334672-chr12:56349611..56350449,2	MCF-7	breast:
2	chr12:56332625..56335607-chr12:56366338..56368554,4	MCF-7	breast:
3	chr12:56122869..56125030-chr12:56332847..56335271,2	K562	blood:
4	chr12:56324513..56325140-chr12:56333753..56334766,3	MCF-7	breast:
5	chr12:56332251..56334580-chr12:56358536..56360583,2	MCF-7	breast:
6	chr12:56216446..56218890-chr12:56332823..56335232,2	K562	blood:
7	chr12:56122789..56124369-chr12:56333771..56335626,2	K562	blood:
8	chr12:56135076..56137351-chr12:56332808..56335651,3	K562	blood:
9	chr12:56330972..56338064-chr12:56344899..56352450,13	MCF-7	breast:
10	chr12:56333047..56336022-chr12:56349677..56352067,3	K562	blood:
11	chr12:56229943..56232528-chr12:56333269..56336105,2	MCF-7	breast:
12	chr12:56225833..56228193-chr12:56331693..56334931,3	MCF-7	breast:
13	chr12:56211687..56216264-chr12:56332406..56336008,6	MCF-7	breast:
14	chr12:56334256..56336718-chr12:56359485..56361088,3	K562	blood:
15	chr12:56333191..56336155-chr12:56365028..56368008,4	K562	blood:
16	chr12:56222874..56225459-chr12:56331362..56334369,4	MCF-7	breast:
17	chr12:56135076..56139517-chr12:56332723..56335701,7	K562	blood:
18	chr12:56332717..56336094-chr12:56364167..56367444,3	K562	blood:

No data

Variant related genes	Relation type
DGKA	TF binding region
ENSG00000123374	Chromatin interaction
ENSG00000123342	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000135414	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1068188	1.00[ASN][1000 genomes]
rs1088050	1.00[ASN][1000 genomes]
rs11829187	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11829961	0.83[AMR][1000 genomes]
rs11831133	1.00[ASN][1000 genomes]
rs11833164	1.00[ASN][1000 genomes]
rs11834873	1.00[ASN][1000 genomes]
rs11838363	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1681071	1.00[ASN][1000 genomes]
rs1681079	1.00[ASN][1000 genomes]
rs1681080	1.00[ASN][1000 genomes]
rs1681088	1.00[ASN][1000 genomes]
rs1689508	1.00[ASN][1000 genomes]
rs1689509	1.00[ASN][1000 genomes]
rs1701702	1.00[ASN][1000 genomes]
rs2046293	1.00[ASN][1000 genomes]
rs2625137	1.00[ASN][1000 genomes]
rs2625146	1.00[ASN][1000 genomes]
rs2640568	1.00[ASN][1000 genomes]
rs57785224	1.00[ASN][1000 genomes]
rs705697	1.00[ASN][1000 genomes]
rs705710	1.00[ASN][1000 genomes]
rs705712	1.00[ASN][1000 genomes]
rs705713	1.00[ASN][1000 genomes]
rs705714	1.00[ASN][1000 genomes]
rs705716	1.00[ASN][1000 genomes]
rs705717	1.00[ASN][1000 genomes]
rs73336399	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73336402	1.00[ASN][1000 genomes]
rs772463	1.00[ASN][1000 genomes]
rs772464	1.00[ASN][1000 genomes]
rs772697	1.00[ASN][1000 genomes]
rs772698	1.00[ASN][1000 genomes]
rs772701	1.00[ASN][1000 genomes]
rs772705	1.00[ASN][1000 genomes]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56326400-56345000	Weak transcription	Ovary	ovary
2	chr12:56326800-56335800	Weak transcription	Aorta	Aorta
3	chr12:56328600-56335000	Genic enhancers	HMEC	breast
4	chr12:56328800-56352200	Weak transcription	Small Intestine	intestine
5	chr12:56330000-56334400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:56330000-56336000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr12:56330200-56334400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:56330200-56336600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:56330400-56335600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:56330400-56336000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr12:56330400-56339200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:56330400-56339400	Strong transcription	Primary hematopoietic stem cells	blood
13	chr12:56330600-56334600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:56331400-56334600	Genic enhancers	Esophagus	oesophagus
15	chr12:56331600-56335200	Weak transcription	HSMMtube	muscle
16	chr12:56332000-56334600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:56332000-56339800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:56332800-56334400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:56332800-56334600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:56332800-56335000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:56333000-56334600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:56333200-56334600	Enhancers	Stomach Mucosa	stomach
23	chr12:56333400-56334600	Genic enhancers	Colonic Mucosa	Colon
24	chr12:56333400-56334800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:56333600-56334400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:56333600-56334400	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr12:56333600-56334400	Genic enhancers	Gastric	stomach
28	chr12:56333600-56334600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:56333600-56334600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:56333600-56334600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr12:56333600-56334600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:56333600-56334600	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr12:56333600-56334600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:56333600-56334600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:56333600-56334600	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr12:56333600-56334600	Enhancers	Pancreas	Pancrea
37	chr12:56333600-56334600	Genic enhancers	Dnd41	blood
38	chr12:56333600-56334600	Genic enhancers	GM12878-XiMat	blood
39	chr12:56333600-56334600	Flanking Active TSS	Hela-S3	cervix
40	chr12:56333600-56334600	Genic enhancers	NHLF	lung
41	chr12:56333600-56334600	Enhancers	Osteobl	bone
42	chr12:56333600-56334800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:56333600-56335000	Enhancers	Fetal Brain Male	brain
44	chr12:56333800-56334400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr12:56333800-56334400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:56333800-56334400	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr12:56333800-56334400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:56333800-56334400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:56333800-56334400	Enhancers	Liver	Liver
50	chr12:56333800-56334400	Flanking Active TSS	Brain Angular Gyrus	brain

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