Variant report

Variant	rs536904959
Chromosome Location	chr12:56121680-56121681
allele	G/T
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	NFIC	chr12:56121508-56122462	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr12:56121649-56121967	IMR90	lung:	n/a	n/a
3	POLR2A	chr12:56121103-56124569	IMR90	lung:	n/a	n/a
4	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
5	ELF1	chr12:56121482-56122434	K562	blood:	n/a	chr12:56122347-56122359 chr12:56121537-56121548
6	TBL1XR1	chr12:56121561-56121999	K562	blood:	n/a	n/a
7	ELF1	chr12:56121370-56122404	MCF-7	breast:	n/a	chr12:56122347-56122359 chr12:56121537-56121548
8	POLR2A	chr12:56121349-56124018	K562	blood:	n/a	n/a
9	CHD1	chr12:56120323-56124349	IMR90	lung:	n/a	n/a
10	RCOR1	chr12:56121359-56121977	K562	blood:	n/a	n/a
11	POLR2A	chr12:56121588-56123832	Hela-S3	cervix:	n/a	n/a
12	SP1	chr12:56121501-56122524	A549	lung:	n/a	chr12:56122339-56122348 chr12:56122338-56122350 chr12:56122489-56122503 chr12:56122243-56122255 chr12:56122338-56122350 chr12:56122244-56122254 chr12:56122502-56122516 chr12:56122339-56122349 chr12:56122146-56122160 chr12:56122305-56122319 chr12:56121832-56121846 chr12:56122149-56122161 chr12:56122496-56122505 chr12:56122150-56122159 chr12:56122497-56122506 chr12:56122149-56122161 chr12:56122339-56122348 chr12:56122243-56122255 chr12:56122340-56122349 chr12:56122507-56122514
13	TAF1	chr12:56121658-56122230	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr12:56121558-56124313	H1-hESC	embryonic stem cell:	n/a	chr12:56122139-56122150 chr12:56122965-56122974 chr12:56123576-56123584 chr12:56122967-56122976 chr12:56122342-56122353
15	POLR2A	chr12:56121381-56122476	Hela-S3	cervix:	n/a	n/a
16	TEAD4	chr12:56121216-56121979	K562	blood:	n/a	n/a
17	ELF1	chr12:56121328-56124343	GM12878	blood:	n/a	chr12:56122496-56122508 chr12:56122347-56122359 chr12:56121537-56121548 chr12:56122768-56122780 chr12:56122979-56122990
18	EP300	chr12:56121554-56121980	SK-N-SH_RA	brain:	n/a	n/a
19	EP300	chr12:56121648-56122009	SK-N-SH_RA	brain:	n/a	n/a
20	EP300	chr12:56121390-56122509	SK-N-SH	brain:	n/a	chr12:56121538-56121552
21	SMARCB1	chr12:56121492-56123851	Hela-S3	cervix:	n/a	chr12:56122915-56122924
22	TCF12	chr12:56121319-56124183	A549	lung:	n/a	chr12:56122619-56122629
23	REST	chr12:56121315-56121772	K562	blood:	n/a	n/a
24	MXI1	chr12:56121169-56124795	SK-N-SH	brain:	n/a	chr12:56122967-56122976 chr12:56122965-56122974 chr12:56122967-56122976 chr12:56122965-56122974
25	POLR2A	chr12:56121554-56123736	ECC-1	luminal epithelium:	n/a	n/a
26	SIN3AK20	chr12:56121367-56121698	PFSK-1	brain:	n/a	n/a
27	MTA3	chr12:56121529-56122252	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:56120298-56122466	U87	brain:	n/a	n/a
29	ELF1	chr12:56121434-56121966	K562	blood:	n/a	chr12:56121537-56121548
30	MAX	chr12:56121668-56122571	SK-N-SH	brain:	n/a	chr12:56122244-56122254 chr12:56122346-56122356 chr12:56122150-56122160
31	MAX	chr12:56121586-56123871	HCT-116	colon:	n/a	chr12:56122244-56122254 chr12:56122966-56122975 chr12:56122888-56122897 chr12:56122966-56122976 chr12:56122964-56122977 chr12:56122965-56122976 chr12:56122724-56122734 chr12:56122964-56122977 chr12:56122965-56122975 chr12:56122965-56122975 chr12:56122965-56122976 chr12:56122964-56122977 chr12:56122346-56122356 chr12:56122966-56122976 chr12:56122150-56122160 chr12:56122965-56122976
32	GATA2	chr12:56121551-56122077	HUVEC	blood vessel:	n/a	n/a
33	HEY1	chr12:56121414-56121986	K562	blood:	n/a	n/a
34	UBTF	chr12:56121345-56123195	K562	blood:	n/a	n/a
35	POLR2A	chr12:56121518-56122114	HepG2	liver:	n/a	n/a
36	HEY1	chr12:56121672-56121983	K562	blood:	n/a	n/a
37	EP300	chr12:56121475-56122059	K562	blood:	n/a	chr12:56121538-56121552
38	POLR2A	chr12:56121507-56121893	A549	lung:	n/a	n/a
39	POLR2A	chr12:56121229-56122065	K562	blood:	n/a	n/a
40	GATA3	chr12:56121550-56121961	T-47D	breast:	n/a	n/a
41	POLR2A	chr12:56121300-56122484	K562	blood:	n/a	n/a
42	POLR2A	chr12:56121482-56122171	Hela-S3	cervix:	n/a	n/a
43	UBTF	chr12:56121582-56121940	K562	blood:	n/a	n/a
44	EP300	chr12:56121466-56123909	ECC-1	luminal epithelium:	n/a	chr12:56121538-56121552 chr12:56122622-56122638 chr12:56123164-56123180
45	JUND	chr12:56121453-56121972	K562	blood:	n/a	n/a
46	POLR2A	chr12:56121641-56124348	HUVEC	blood vessel:	n/a	n/a
47	SIN3AK20	chr12:56121204-56123972	MCF-7	breast:	n/a	n/a
48	GATA3	chr12:56121263-56122184	MCF-7	breast:	n/a	n/a
49	POLR2A	chr12:56121377-56121852	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:56121511-56124305	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56121253..56122830-chr12:56553054..56555339,2	MCF-7	breast:
2	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
3	chr12:56120003..56122736-chr12:56659216..56661326,3	K562	blood:
4	chr12:56120093..56124486-chr12:56434488..56437037,3	K562	blood:
5	chr12:56120864..56122982-chr12:56435772..56437272,2	MCF-7	breast:
6	chr12:56120515..56122201-chr12:56332595..56334238,2	K562	blood:
7	chr12:56121335..56123958-chr12:56496918..56499786,2	K562	blood:
8	chr12:56120851..56123825-chr12:56659216..56662167,3	K562	blood:
9	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
10	chr12:56098994..56103683-chr12:56119699..56126107,8	MCF-7	breast:
11	chr12:56121086..56122985-chr12:56327062..56330070,3	MCF-7	breast:
12	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
13	chr12:56104896..56106917-chr12:56120568..56123344,2	MCF-7	breast:
14	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
15	chr12:56120591..56123197-chr12:56472700..56474357,3	MCF-7	breast:
16	chr12:56120533..56123958-chr12:56496918..56499602,3	K562	blood:
17	chr12:56119392..56124555-chr12:56134719..56139155,10	MCF-7	breast:
18	chr12:56118873..56123597-chr12:56135421..56141775,11	K562	blood:
19	chr12:56120972..56124195-chr12:56135682..56138639,8	MCF-7	breast:
20	chr12:56121261..56123274-chr12:56389263..56391155,2	K562	blood:
21	chr12:56120505..56122635-chr12:56345271..56347933,2	K562	blood:
22	chr12:56121418..56123151-chr12:56510609..56512159,2	MCF-7	breast:
23	chr12:56120587..56125243-chr12:56320195..56323478,6	MCF-7	breast:
24	chr12:56099553..56102772-chr12:56120884..56124385,4	K562	blood:
25	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:
26	chr12:56121599..56124065-chr12:56209598..56212420,4	MCF-7	breast:
27	chr12:56121284..56123165-chr12:56709581..56711185,2	K562	blood:

Variant related genes	Relation type
ENSG00000258056	TF binding region
CD63	TF binding region
ENSG00000135482	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	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
3	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	esv3406101	chr12:56121510-56124058	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	56 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	chr12:56116600-56121800	Transcr. at gene 5' and 3'	HSMM	muscle
2	chr12:56116600-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:56116800-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:56117600-56122000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr12:56117800-56122200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:56118800-56122000	Transcr. at gene 5' and 3'	NHLF	lung
7	chr12:56119800-56122000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
8	chr12:56120400-56121800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:56120400-56122000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:56120400-56122000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
11	chr12:56120400-56122000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
12	chr12:56120400-56122000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
13	chr12:56120400-56122200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr12:56120600-56121800	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:56120600-56121800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:56120600-56121800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:56120600-56121800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
18	chr12:56120600-56122000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:56120600-56122000	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
20	chr12:56120600-56122000	Transcr. at gene 5' and 3'	NHEK	skin
21	chr12:56120600-56122200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:56120800-56121800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:56120800-56121800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr12:56120800-56121800	Flanking Active TSS	Stomach Mucosa	stomach
25	chr12:56120800-56122000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:56120800-56122000	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
27	chr12:56120800-56122000	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr12:56120800-56122000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
29	chr12:56120800-56122000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
30	chr12:56120800-56122000	Flanking Active TSS	Left Ventricle	heart
31	chr12:56120800-56122000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr12:56121000-56121800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:56121000-56121800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr12:56121000-56121800	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:56121000-56121800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr12:56121000-56121800	Flanking Active TSS	Right Atrium	heart
37	chr12:56121000-56122000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:56121000-56122000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr12:56121000-56122000	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr12:56121000-56122000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr12:56121000-56122000	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr12:56121000-56122000	Flanking Active TSS	Fetal Brain Female	brain
43	chr12:56121000-56122000	Transcr. at gene 5' and 3'	Fetal Lung	lung
44	chr12:56121000-56122000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:56121000-56122000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:56121000-56122200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:56121000-56122200	Flanking Active TSS	Liver	Liver
48	chr12:56121000-56123600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:56121000-56124000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr12:56121000-56124200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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