Variant report

Variant	rs59499104
Chromosome Location	chr12:56545638-56545639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:56545560-56545710	WERI-Rb-1	eye:	n/a	n/a
2	MYC	chr12:56545417-56546498	K562	blood:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
3	MAX	chr12:56545458-56546461	K562	blood:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
4	MYC	chr12:56545490-56546423	K562	blood:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
5	CHD1	chr12:56545456-56546575	GM12878	blood:	n/a	chr12:56546068-56546078
6	CTCF	chr12:56545620-56545770	BJ	skin:	n/a	n/a
7	FOXA1	chr12:56545476-56545793	T-47D	breast:	n/a	n/a
8	POLR2A	chr12:56545357-56546596	PANC-1	pancreas:	n/a	n/a
9	MAX	chr12:56545245-56546776	HCT-116	colon:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
10	POLR2A	chr12:56545443-56546756	H1-neurons	neurons:	n/a	n/a
11	MAX	chr12:56545522-56546507	K562	blood:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
12	BHLHE40	chr12:56545539-56546563	K562	blood:	n/a	chr12:56545996-56546012
13	CTCF	chr12:56545540-56545690	MCF-7	breast:	n/a	n/a
14	CTCF	chr12:56545520-56545670	GM12867	blood:	n/a	n/a
15	CTCF	chr12:56545580-56545730	AG09309	skin:	n/a	n/a
16	CTCF	chr12:56545500-56545650	HCFaa	heart:	n/a	n/a
17	POLR2A	chr12:56545513-56545806	A549	lung:	n/a	n/a
18	YY1	chr12:56545315-56546572	H1-hESC	embryonic stem cell:	n/a	chr12:56546070-56546079 chr12:56546377-56546386 chr12:56546386-56546397
19	CTCF	chr12:56545516-56545687	MCF-7	breast:	n/a	n/a
20	CTCF	chr12:56545500-56545650	BE2_C	brain:	n/a	n/a
21	ZBTB7A	chr12:56545476-56545712	K562	blood:	n/a	n/a
22	CTCF	chr12:56545520-56545670	BE2_C	brain:	n/a	n/a
23	POLR2A	chr12:56545413-56546546	GM12892	blood:	n/a	n/a
24	POLR2A	chr12:56545292-56546622	GM12878	blood:	n/a	n/a
25	YY1	chr12:56545452-56545876	HCT-116	colon:	n/a	n/a
26	HEY1	chr12:56545271-56546460	K562	blood:	n/a	n/a
27	POLR2A	chr12:56545422-56546362	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr12:56545540-56545690	HL-60	blood:	n/a	n/a
29	FOXA1	chr12:56545468-56545790	T-47D	breast:	n/a	n/a
30	NFATC1	chr12:56545538-56546200	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:56545228-56546877	K562	blood:	n/a	n/a
32	CTCF	chr12:56545500-56545650	NB4	blood:	n/a	n/a
33	CTCF	chr12:56545520-56545670	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:56545492-56546567	HUVEC	blood vessel:	n/a	n/a
35	MAFK	chr12:56545595-56545675	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:56545331-56546477	GM12892	blood:	n/a	n/a
37	CTCF	chr12:56545560-56545710	HBMEC	blood vessel:	n/a	n/a
38	SIN3A	chr12:56545429-56546699	H1-hESC	embryonic stem cell:	n/a	chr12:56545578-56545587 chr12:56546022-56546036
39	FOS	chr12:56545542-56546498	HUVEC	blood vessel:	n/a	chr12:56546219-56546229 chr12:56546066-56546075 chr12:56546220-56546228 chr12:56546219-56546229 chr12:56546218-56546229 chr12:56546219-56546229 chr12:56546219-56546229 chr12:56546216-56546227
40	GTF2B	chr12:56545443-56546370	K562	blood:	n/a	n/a
41	POLR2A	chr12:56545461-56545911	A549	lung:	n/a	n/a
42	CTCF	chr12:56545560-56545710	GM06990	blood:	n/a	n/a
43	CTCF	chr12:56545541-56545703	Lung_OC	lung:	n/a	n/a
44	CTCF	chr12:56545402-56545748	K562	blood:	n/a	n/a
45	MAZ	chr12:56545558-56547488	IMR90	lung:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
46	POLR2A	chr12:56545313-56546590	HepG2	liver:	n/a	n/a
47	MYBL2	chr12:56545335-56546543	HepG2	liver:	n/a	n/a
48	CTCF	chr12:56545540-56545690	SK-N-SH_RA	brain:	n/a	n/a
49	REST	chr12:56545436-56546693	A549	lung:	n/a	chr12:56546328-56546341 chr12:56546551-56546558
50	CTCF	chr12:56545540-56545690	HPF	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56543805..56547677-chr12:56615744..56618519,4	MCF-7	breast:
2	chr12:56434536..56437733-chr12:56543304..56547761,4	K562	blood:
3	chr12:56543953..56550163-chr12:56578779..56585351,11	MCF-7	breast:
4	chr12:56545189..56545979-chr3:73159940..73160591,2	Hela-S3	cervix:
5	chr12:56472620..56475817-chr12:56544405..56546973,4	MCF-7	breast:
6	chr12:56530580..56533098-chr12:56544612..56547125,6	MCF-7	breast:
7	chr12:56543262..56546073-chr12:56618060..56619821,2	K562	blood:
8	chr12:56509009..56513573-chr12:56543891..56549811,15	MCF-7	breast:
9	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
10	chr12:56544479..56547707-chr17:57917594..57920686,3	MCF-7	breast:
11	chr12:56545246..56546002-chr5:95997996..95998522,2	Hela-S3	cervix:
12	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:
13	chr12:56471831..56474623-chr12:56543968..56546467,2	K562	blood:
14	chr12:56497691..56500664-chr12:56545558..56547668,3	MCF-7	breast:
15	chr12:56471798..56475584-chr12:56544179..56549010,6	MCF-7	breast:
16	chr12:56544606..56546956-chr12:56708353..56710252,2	K562	blood:
17	chr12:56434062..56437733-chr12:56543304..56547386,5	K562	blood:

Variant related genes	Relation type
MYL6B	TF binding region
ENSG00000258345	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000153113	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11171760	1.00[EUR][1000 genomes]
rs11171772	1.00[AMR][1000 genomes]
rs11837267	1.00[EUR][1000 genomes]
rs12298822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12306670	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12308473	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12316272	0.84[AFR][1000 genomes]
rs12320265	1.00[AMR][1000 genomes]
rs1405859	1.00[AMR][1000 genomes]
rs17852368	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2450101	1.00[EUR][1000 genomes]
rs2629453	1.00[EUR][1000 genomes]
rs28546848	1.00[EUR][1000 genomes]
rs55887836	1.00[AMR][1000 genomes]
rs56163805	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60011575	0.81[AFR][1000 genomes]
rs7136420	1.00[AMR][1000 genomes]
rs73340385	1.00[EUR][1000 genomes]
rs73340390	1.00[EUR][1000 genomes]
rs7397951	1.00[EUR][1000 genomes]
rs74092003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772925	1.00[EUR][1000 genomes]
rs772926	1.00[EUR][1000 genomes]
rs773654	1.00[EUR][1000 genomes]
rs773663	1.00[EUR][1000 genomes]
rs7967464	1.00[EUR][1000 genomes]
rs7975486	1.00[EUR][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56545200-56545800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:56545200-56545800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:56545200-56545800	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr12:56545200-56545800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:56545200-56545800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:56545200-56545800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:56545200-56545800	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr12:56545200-56545800	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr12:56545200-56545800	Flanking Active TSS	Colonic Mucosa	Colon
10	chr12:56545200-56545800	Flanking Active TSS	Colon Smooth Muscle	Colon
11	chr12:56545200-56545800	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr12:56545200-56545800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:56545200-56545800	Flanking Active TSS	Fetal Brain Female	brain
14	chr12:56545200-56545800	Flanking Active TSS	Fetal Kidney	kidney
15	chr12:56545200-56545800	Flanking Active TSS	Fetal Lung	lung
16	chr12:56545200-56545800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr12:56545200-56545800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:56545200-56545800	Flanking Active TSS	Dnd41	blood
19	chr12:56545200-56545800	Flanking Active TSS	HSMMtube	muscle
20	chr12:56545200-56545800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:56545200-56546000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:56545200-56546000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:56545200-56546000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:56545200-56546000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr12:56545200-56546000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr12:56545200-56546000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr12:56545200-56546000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr12:56545200-56546000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr12:56545200-56546000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr12:56545200-56546000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:56545200-56546000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:56545200-56546000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:56545200-56546000	Flanking Active TSS	Liver	Liver
34	chr12:56545200-56546000	Flanking Active TSS	Fetal Thymus	thymus
35	chr12:56545200-56546000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr12:56545200-56546000	Flanking Active TSS	Hela-S3	cervix
37	chr12:56545200-56546000	Flanking Active TSS	HSMM	muscle
38	chr12:56545200-56546000	Flanking Active TSS	NH-A	brain
39	chr12:56545200-56546200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:56545200-56546200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:56545200-56546600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:56545200-56546600	Active TSS	Rectal Smooth Muscle	rectum
43	chr12:56545200-56546800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr12:56545200-56546800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr12:56545200-56546800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr12:56545200-56547000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr12:56545200-56547200	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr12:56545200-56547200	Active TSS	H9 Cell Line	embryonic stem cell
49	chr12:56545200-56547400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:56545200-56547600	Active TSS	iPS-15b Cell Line	embryonic stem cell

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