Variant report

Variant	rs2069398
Chromosome Location	chr12:56360876-56360877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:164)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:164 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr12:56360430-56361245	GM12878	blood:	n/a	n/a
2	MTA3	chr12:56359891-56361091	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr12:56359786-56360979	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr12:56360374-56361008	SK-N-SH	brain:	n/a	chr12:56360501-56360511
5	MAX	chr12:56360219-56361159	K562	blood:	n/a	chr12:56360501-56360511
6	SIN3AK20	chr12:56360501-56361041	PANC-1	pancreas:	n/a	n/a
7	SMC3	chr12:56360097-56361165	Hela-S3	cervix:	n/a	chr12:56360578-56360585 chr12:56360533-56360543
8	POLR2A	chr12:56359858-56361309	Hela-S3	cervix:	n/a	n/a
9	IRF1	chr12:56360113-56360972	K562	blood:	n/a	chr12:56360535-56360549 chr12:56360564-56360578
10	REST	chr12:56360137-56360933	A549	lung:	n/a	chr12:56360261-56360274
11	POLR2A	chr12:56360261-56361002	U87	brain:	n/a	n/a
12	POLR2A	chr12:56360113-56361021	ProgFib	skin:	n/a	n/a
13	PML	chr12:56360098-56360879	MCF-7	breast:	n/a	n/a
14	SMARCC1	chr12:56359755-56361790	Hela-S3	cervix:	n/a	n/a
15	FOXM1	chr12:56360239-56361098	GM12878	blood:	n/a	n/a
16	CHD2	chr12:56360223-56361255	GM12878	blood:	n/a	n/a
17	MAX	chr12:56360295-56361081	MCF-7	breast:	n/a	chr12:56360501-56360511
18	HEY1	chr12:56359866-56361298	K562	blood:	n/a	n/a
19	RUNX3	chr12:56360304-56361109	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:56360052-56360936	HL-60	blood:	n/a	n/a
21	POLR2A	chr12:56360018-56361753	IMR90	lung:	n/a	n/a
22	BHLHE40	chr12:56360800-56361036	K562	blood:	n/a	n/a
23	MAX	chr12:56360237-56361030	K562	blood:	n/a	chr12:56360501-56360511
24	POLR2A	chr12:56360250-56361028	GM18951	blood:	n/a	n/a
25	POLR2A	chr12:56359849-56361144	K562	blood:	n/a	n/a
26	MAX	chr12:56360226-56361201	A549	lung:	n/a	chr12:56360501-56360511
27	MAZ	chr12:56360278-56361179	K562	blood:	n/a	chr12:56360501-56360511
28	TCF12	chr12:56360034-56360879	ECC-1	luminal epithelium:	n/a	chr12:56360267-56360277
29	TAF1	chr12:56359650-56361028	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:56359846-56361008	HepG2	liver:	n/a	n/a
31	SIN3AK20	chr12:56360435-56361037	K562	blood:	n/a	n/a
32	POLR2A	chr12:56360218-56360945	GM18526	blood:	n/a	n/a
33	ZBTB7A	chr12:56360342-56361060	K562	blood:	n/a	n/a
34	CREB1	chr12:56360274-56360957	A549	lung:	n/a	n/a
35	MXI1	chr12:56359946-56362001	IMR90	lung:	n/a	chr12:56360268-56360277
36	ELF1	chr12:56360854-56361057	HepG2	liver:	n/a	chr12:56360992-56361005
37	FOXA2	chr12:56360519-56361085	A549	lung:	n/a	n/a
38	TCF12	chr12:56360198-56361045	ECC-1	luminal epithelium:	n/a	chr12:56360267-56360277
39	POLR2A	chr12:56360206-56361090	GM19099	blood:	n/a	n/a
40	ZBTB7A	chr12:56360187-56361455	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr12:56359594-56361350	ECC-1	luminal epithelium:	n/a	n/a
42	TAF1	chr12:56360196-56361345	ECC-1	luminal epithelium:	n/a	n/a
43	TAF1	chr12:56360103-56361272	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr12:56359974-56361112	NB4	blood:	n/a	n/a
45	MAX	chr12:56360295-56361107	A549	lung:	n/a	chr12:56360501-56360511
46	TFAP2A	chr12:56360143-56360901	Hela-S3	cervix:	n/a	chr12:56360459-56360469 chr12:56360457-56360471 chr12:56360459-56360469 chr12:56360531-56360543 chr12:56360531-56360542 chr12:56360499-56360510 chr12:56360459-56360471 chr12:56360459-56360469 chr12:56360459-56360469
47	POLR2A	chr12:56360158-56360912	MCF-7	breast:	n/a	n/a
48	ELF1	chr12:56360785-56361221	K562	blood:	n/a	chr12:56360992-56361005
49	FOXA1	chr12:56360430-56361100	HepG2	liver:	n/a	n/a
50	FOXA1	chr12:56360597-56360973	HepG2	liver:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56360664..56361305-chr16:402190..403012,2	MCF-7	breast:
2	chr12:56360588..56363018-chr12:56383042..56385730,2	K562	blood:
3	chr12:56351426..56355339-chr12:56358310..56361732,4	K562	blood:
4	chr12:56348195..56352007-chr12:56357444..56361194,9	MCF-7	breast:
5	chr12:56132724..56138260-chr12:56359199..56362083,4	MCF-7	breast:
6	chr12:56360360..56361134-chr18:812306..813264,2	Hela-S3	cervix:
7	chr12:56319178..56327497-chr12:56356755..56363470,19	MCF-7	breast:
8	chr12:56319082..56322613-chr12:56358459..56362927,5	MCF-7	breast:
9	chr12:56360414..56361023-chr9:98079688..98080296,2	Hela-S3	cervix:
10	chr12:56359297..56361313-chr17:56079815..56082507,2	MCF-7	breast:
11	chr12:56135390..56138217-chr12:56359317..56362756,4	K562	blood:
12	chr12:56325013..56327160-chr12:56358376..56361876,4	MCF-7	breast:
13	chr12:56360275..56361250-chr6:111804421..111805081,2	Hela-S3	cervix:
14	chr12:56208204..56214844-chr12:56359426..56363484,9	MCF-7	breast:
15	chr12:56360672..56362289-chr12:56400535..56402399,2	MCF-7	breast:
16	chr12:56334256..56336718-chr12:56359485..56361088,3	K562	blood:
17	chr12:56222629..56224210-chr12:56360476..56363033,2	MCF-7	breast:
18	chr12:56360287..56361178-chr3:49711127..49711777,2	Hela-S3	cervix:
19	chr12:56319307..56323047-chr12:56359033..56361996,7	K562	blood:
20	chr12:56357871..56361008-chr12:56510432..56513466,3	K562	blood:
21	chr12:56326452..56329346-chr12:56360017..56362575,2	K562	blood:
22	chr12:56328814..56332506-chr12:56359675..56362006,3	MCF-7	breast:
23	chr12:56360017..56362011-chr12:56434506..56437466,2	K562	blood:
24	chr12:56360624..56364064-chr12:56389013..56391447,3	K562	blood:
25	chr12:56318129..56322590-chr12:56359033..56362321,5	K562	blood:
26	chr12:56359758..56363158-chr12:56433727..56437301,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WIBG-1	chr12:56360622-56360946	ENSG00000258554.1

No data

Variant related genes	Relation type
CDK2	TF binding region
PMEL	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000231889	Chromatin interaction
ENSG00000136450	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000103126	Chromatin interaction
ENSG00000009413	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000176105	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000205323	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11171705	0.98[EUR][1000 genomes]
rs12307952	0.98[EUR][1000 genomes]
rs12309895	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2069391	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3213122	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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	189 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	chr12:56358000-56363200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:56358600-56361200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:56358800-56361800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:56359000-56361400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:56359000-56361400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:56359000-56361600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr12:56359200-56361400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56359200-56361600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:56359400-56361400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr12:56359600-56361400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:56359600-56361600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:56359800-56361400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr12:56359800-56361600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:56359800-56361600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr12:56359800-56361800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:56359800-56361800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:56360000-56361000	Active TSS	Ovary	ovary
18	chr12:56360000-56361000	Active TSS	Spleen	Spleen
19	chr12:56360000-56361200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:56360000-56361200	Active TSS	Aorta	Aorta
21	chr12:56360000-56361200	Active TSS	Psoas Muscle	Psoas
22	chr12:56360000-56361200	Active TSS	Right Atrium	heart
23	chr12:56360000-56361400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr12:56360000-56361400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:56360000-56361400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:56360000-56361800	Active TSS	Fetal Brain Female	brain
27	chr12:56360000-56361800	Active TSS	Fetal Muscle Trunk	muscle
28	chr12:56360200-56361000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:56360200-56361000	Active TSS	Brain Anterior Caudate	brain
30	chr12:56360200-56361000	Active TSS	Brain Hippocampus Middle	brain
31	chr12:56360200-56361000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:56360200-56361000	Active TSS	Brain Substantia Nigra	brain
33	chr12:56360200-56361000	Active TSS	Duodenum Mucosa	Duodenum
34	chr12:56360200-56361000	Active TSS	Fetal Intestine Large	intestine
35	chr12:56360200-56361000	Active TSS	Pancreas	Pancrea
36	chr12:56360200-56361000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:56360200-56361000	Active TSS	Thymus	Thymus
38	chr12:56360200-56361000	Bivalent/Poised TSS	HepG2	liver
39	chr12:56360200-56361200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:56360200-56361200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:56360200-56361200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:56360200-56361200	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:56360200-56361200	Active TSS	Fetal Intestine Small	intestine
44	chr12:56360200-56361200	Active TSS	Fetal Lung	lung
45	chr12:56360200-56361200	Active TSS	Gastric	stomach
46	chr12:56360200-56361200	Active TSS	Left Ventricle	heart
47	chr12:56360200-56361200	Active TSS	Lung	lung
48	chr12:56360200-56361200	Active TSS	Right Ventricle	heart
49	chr12:56360200-56361200	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr12:56360200-56361200	Active TSS	Small Intestine	intestine

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