Variant report

Variant	rs558483897
Chromosome Location	chr12:57482464-57482465
allele	C/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	PML	chr12:57481509-57483132	MCF-7	breast:	n/a	n/a
2	TBL1XR1	chr12:57480142-57482871	GM12878	blood:	n/a	n/a
3	TAF1	chr12:57481569-57482612	PFSK-1	brain:	n/a	n/a
4	GATA3	chr12:57480797-57483098	MCF-7	breast:	n/a	n/a
5	SMARCC1	chr12:57481280-57482541	Hela-S3	cervix:	n/a	n/a
6	SIN3AK20	chr12:57480221-57484098	MCF-7	breast:	n/a	n/a
7	TAF1	chr12:57482203-57482484	GM12878	blood:	n/a	n/a
8	FOS	chr12:57482243-57482537	MCF10A-Er-Src	breast:	n/a	n/a
9	TAF1	chr12:57482088-57482621	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:57479357-57482603	SK-N-MC	brain:	n/a	n/a
11	NR3C1	chr12:57482189-57482618	A549	lung:	n/a	n/a
12	USF1	chr12:57482289-57482610	GM12878	blood:	n/a	n/a
13	MAX	chr12:57481506-57483316	HepG2	liver:	n/a	chr12:57482476-57482487 chr12:57482875-57482885 chr12:57481781-57481791 chr12:57481834-57481842 chr12:57482520-57482529 chr12:57481680-57481690 chr12:57483153-57483163
14	HEY1	chr12:57480273-57482609	K562	blood:	n/a	chr12:57480500-57480515
15	POLR2A	chr12:57482156-57483151	H1-neurons	neurons:	n/a	n/a
16	SIN3AK20	chr12:57482182-57482544	PFSK-1	brain:	n/a	n/a
17	BCLAF1	chr12:57481625-57482613	GM12878	blood:	n/a	chr12:57481821-57481830 chr12:57482546-57482559
18	MYC	chr12:57479741-57483065	K562	blood:	n/a	chr12:57481172-57481182 chr12:57482476-57482487 chr12:57482875-57482885 chr12:57481174-57481181 chr12:57480313-57480323 chr12:57481781-57481791 chr12:57481093-57481103 chr12:57481834-57481842 chr12:57481164-57481174 chr12:57482520-57482529 chr12:57481680-57481690 chr12:57481172-57481183
19	EGR1	chr12:57482133-57483157	MCF-7	breast:	n/a	chr12:57482835-57482844 chr12:57482833-57482844 chr12:57482832-57482845 chr12:57482519-57482530 chr12:57482518-57482531 chr12:57482835-57482845 chr12:57482567-57482577 chr12:57482834-57482844 chr12:57482832-57482846 chr12:57482520-57482530 chr12:57482518-57482531 chr12:57482519-57482533 chr12:57482520-57482530 chr12:57482878-57482888 chr12:57482834-57482844 chr12:57482832-57482845 chr12:57482441-57482454 chr12:57482832-57482845 chr12:57482518-57482532 chr12:57482828-57482850 chr12:57482838-57482851 chr12:57482831-57482846 chr12:57482832-57482845 chr12:57482519-57482530 chr12:57482521-57482530
20	EP300	chr12:57482150-57482856	MCF-7	breast:	n/a	n/a
21	HDAC2	chr12:57481421-57482706	HepG2	liver:	n/a	n/a
22	TAF1	chr12:57482191-57482515	GM12891	blood:	n/a	n/a
23	EP300	chr12:57481477-57483142	MCF-7	breast:	n/a	chr12:57482999-57483015 chr12:57481959-57481969
24	ETS1	chr12:57481847-57482622	A549	lung:	n/a	chr12:57482505-57482522 chr12:57482546-57482557 chr12:57482505-57482522
25	NFIC	chr12:57482249-57482626	HepG2	liver:	n/a	n/a
26	PAX5	chr12:57482299-57482630	GM12892	blood:	n/a	n/a
27	E2F6	chr12:57482221-57482614	K562	blood:	n/a	chr12:57482546-57482555 chr12:57482465-57482474 chr12:57482491-57482506
28	POLR2A	chr12:57479540-57482719	GM12878	blood:	n/a	n/a
29	BCL3	chr12:57482139-57482615	GM12878	blood:	n/a	chr12:57482546-57482559
30	ZKSCAN1	chr12:57481361-57482576	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chr12:57482214-57482610	HepG2	liver:	n/a	n/a
32	CTCF	chr12:57482320-57482470	SK-N-SH_RA	brain:	n/a	n/a
33	CEBPB	chr12:57482080-57482609	K562	blood:	n/a	n/a
34	USF1	chr12:57482150-57482623	A549	lung:	n/a	n/a
35	TCF7L2	chr12:57481721-57482519	Hela-S3	cervix:	n/a	n/a
36	USF1	chr12:57482143-57482723	SK-N-SH	brain:	n/a	n/a
37	FOXA1	chr12:57482138-57482622	HepG2	liver:	n/a	n/a
38	E2F6	chr12:57481907-57482663	A549	lung:	n/a	chr12:57482546-57482555 chr12:57482465-57482474 chr12:57482491-57482506
39	POLR2A	chr12:57481165-57482591	GM12891	blood:	n/a	n/a
40	REST	chr12:57481181-57482609	A549	lung:	n/a	chr12:57481761-57481774 chr12:57481537-57481555 chr12:57482236-57482254 chr12:57481186-57481199
41	TAF1	chr12:57481492-57482561	A549	lung:	n/a	n/a
42	ESR1	chr12:57482314-57482739	ECC-1	luminal epithelium:	n/a	chr12:57482583-57482598
43	FOXP2	chr12:57482236-57482554	SK-N-MC	brain:	n/a	n/a
44	SIN3AK20	chr12:57482169-57482656	K562	blood:	n/a	n/a
45	BHLHE40	chr12:57481905-57482948	HepG2	liver:	n/a	n/a
46	CEBPB	chr12:57482158-57482625	HepG2	liver:	n/a	n/a
47	TAF1	chr12:57480573-57482679	ECC-1	luminal epithelium:	n/a	n/a
48	ZNF143	chr12:57482286-57482477	K562	blood:	n/a	n/a
49	FOXA2	chr12:57481662-57482681	A549	lung:	n/a	n/a
50	MYC	chr12:57482372-57482580	K562	blood:	n/a	chr12:57482476-57482487 chr12:57482520-57482529

No.	Distal block	Cell Line	Cell type
1	chr12:57480730..57482980-chr22:30821436..30824082,2	MCF-7	breast:
2	chr12:57398945..57400725-chr12:57479656..57482846,3	MCF-7	breast:
3	chr12:56473732..56475652-chr12:57482023..57483860,2	MCF-7	breast:
4	chr12:57480746..57483234-chr12:57915069..57916762,2	MCF-7	breast:
5	chr12:57143938..57146732-chr12:57482240..57484256,2	MCF-7	breast:
6	chr12:57480720..57482842-chr12:58137848..58140572,2	MCF-7	breast:
7	chr12:57118003..57119898-chr12:57480309..57484526,4	K562	blood:
8	chr12:57422175..57424146-chr12:57481515..57483170,2	MCF-7	breast:
9	chr12:57022390..57024526-chr12:57480119..57483489,4	MCF-7	breast:
10	chr12:57480017..57482545-chr14:24683866..24686216,2	MCF-7	breast:
11	chr11:126173346..126174012-chr12:57481744..57482542,2	Hela-S3	cervix:
12	chr12:57478737..57483929-chr12:57633097..57638164,8	MCF-7	breast:
13	chr12:57479977..57484073-chr12:57519609..57523791,10	MCF-7	breast:
14	chr12:57116631..57120456-chr12:57479265..57482503,6	MCF-7	breast:
15	chr12:57481012..57482707-chr3:64002867..64005175,2	MCF-7	breast:
16	chr12:57385703..57388264-chr12:57481294..57482820,2	K562	blood:
17	chr12:57144616..57146221-chr12:57481056..57483916,2	K562	blood:
18	chr12:57482277..57484373-chr12:57520375..57523117,3	MCF-7	breast:
19	chr12:57481564..57482544-chr17:8076551..8077091,2	Hela-S3	cervix:
20	chr12:57480031..57482599-chr12:58144777..58147375,2	MCF-7	breast:
21	chr12:57143195..57148502-chr12:57480974..57485182,5	K562	blood:
22	chr12:56511049..56513507-chr12:57480483..57482738,2	MCF-7	breast:
23	chr12:57026457..57031197-chr12:57479410..57483153,5	MCF-7	breast:
24	chr12:57080529..57082220-chr12:57480203..57482961,2	MCF-7	breast:
25	chr12:57481778..57482507-chr3:119812302..119813196,2	Hela-S3	cervix:
26	chr12:57117875..57121156-chr12:57480482..57484573,7	MCF-7	breast:
27	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:
28	chr12:57480219..57483297-chr12:57622863..57624907,4	MCF-7	breast:
29	chr12:57482175..57482736-chr19:39897077..39898067,2	Hela-S3	cervix:
30	chr12:57481972..57484968-chr12:57912943..57915711,3	K562	blood:
31	chr12:57480714..57483772-chr12:57558111..57562184,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NAB2-1	chr12:57481380-57482632	XLOC_009777

Variant related genes	Relation type
TMEM194A	TF binding region
NAB2	TF binding region
ENSG00000242114	Chromatin interaction
ENSG00000260669	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000166860	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000166863	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000166856	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000182199	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000110063	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000198056	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv3374301	chr12:57481510-57484058	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 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	chr12:57480000-57483800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:57480000-57484000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:57480000-57484400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:57480000-57484400	Active TSS	Aorta	Aorta
5	chr12:57480000-57484400	Active TSS	Left Ventricle	heart
6	chr12:57480000-57484400	Active TSS	Right Atrium	heart
7	chr12:57480000-57485200	Active TSS	Psoas Muscle	Psoas
8	chr12:57480200-57483800	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr12:57480200-57484000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:57480200-57484000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:57480200-57484000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:57480200-57484000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:57480200-57484400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr12:57480200-57484400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:57480200-57484400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:57480200-57484400	Active TSS	Brain Anterior Caudate	brain
17	chr12:57480200-57484400	Active TSS	Lung	lung
18	chr12:57480200-57484600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:57480400-57483600	Active TSS	Spleen	Spleen
20	chr12:57480400-57483800	Active TSS	Brain Cingulate Gyrus	brain
21	chr12:57480400-57483800	Active TSS	Small Intestine	intestine
22	chr12:57480400-57484400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:57480400-57484400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:57480400-57484400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr12:57480400-57484400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr12:57480400-57484400	Active TSS	Esophagus	oesophagus
27	chr12:57480400-57484400	Active TSS	Right Ventricle	heart
28	chr12:57480400-57484600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:57480400-57485000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:57480600-57483600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:57480600-57483800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:57480600-57484000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:57480600-57484200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:57480600-57484400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:57480600-57484400	Active TSS	Colon Smooth Muscle	Colon
36	chr12:57480600-57484400	Active TSS	Thymus	Thymus
37	chr12:57480600-57484600	Active TSS	Ovary	ovary
38	chr12:57480800-57483600	Active TSS	Fetal Stomach	stomach
39	chr12:57480800-57483800	Active TSS	Gastric	stomach
40	chr12:57480800-57484800	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr12:57480800-57485000	Active TSS	Fetal Kidney	kidney
42	chr12:57481200-57482600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr12:57481200-57482600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:57481200-57482600	Flanking Active TSS	Colonic Mucosa	Colon
45	chr12:57481200-57482600	Flanking Active TSS	HMEC	breast
46	chr12:57481400-57482600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr12:57481600-57482600	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr12:57481600-57482600	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr12:57481600-57482600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr12:57481800-57482600	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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