Variant report

Variant	rs550556558
Chromosome Location	chr12:57481559-57481560
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	PML	chr12:57481509-57483132	MCF-7	breast:	n/a	n/a
2	TBL1XR1	chr12:57480142-57482871	GM12878	blood:	n/a	n/a
3	GATA3	chr12:57480797-57483098	MCF-7	breast:	n/a	n/a
4	SMARCC1	chr12:57481280-57482541	Hela-S3	cervix:	n/a	n/a
5	EGR1	chr12:57480906-57481927	H1-hESC	embryonic stem cell:	n/a	chr12:57481121-57481131 chr12:57481095-57481108 chr12:57481707-57481721 chr12:57481115-57481137 chr12:57481119-57481132 chr12:57481148-57481161 chr12:57481121-57481130 chr12:57481228-57481238 chr12:57481120-57481131 chr12:57481079-57481089 chr12:57481627-57481640 chr12:57481619-57481629 chr12:57481118-57481133 chr12:57481122-57481131 chr12:57481120-57481131 chr12:57481681-57481691 chr12:57481119-57481132 chr12:57481229-57481239 chr12:57481121-57481131 chr12:57481119-57481133 chr12:57481119-57481132 chr12:57481017-57481031 chr12:57481119-57481132 chr12:57481243-57481256 chr12:57481503-57481527
6	SIN3AK20	chr12:57480221-57484098	MCF-7	breast:	n/a	n/a
7	EP300	chr12:57480962-57482127	ECC-1	luminal epithelium:	n/a	chr12:57481186-57481202 chr12:57481959-57481969
8	POLR2A	chr12:57481400-57482086	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:57479357-57482603	SK-N-MC	brain:	n/a	n/a
10	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
11	HEY1	chr12:57480273-57482609	K562	blood:	n/a	chr12:57480500-57480515
12	TAF1	chr12:57481287-57481588	GM12878	blood:	n/a	n/a
13	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
14	HDAC2	chr12:57481421-57482706	HepG2	liver:	n/a	n/a
15	EP300	chr12:57481477-57483142	MCF-7	breast:	n/a	chr12:57482999-57483015 chr12:57481959-57481969
16	POLR2A	chr12:57479540-57482719	GM12878	blood:	n/a	n/a
17	ZKSCAN1	chr12:57481361-57482576	Hela-S3	cervix:	n/a	n/a
18	TAF1	chr12:57481358-57482028	K562	blood:	n/a	n/a
19	USF1	chr12:57480905-57481983	ECC-1	luminal epithelium:	n/a	chr12:57481185-57481201 chr12:57481193-57481209
20	POLR2A	chr12:57481165-57482591	GM12891	blood:	n/a	n/a
21	REST	chr12:57481181-57482609	A549	lung:	n/a	chr12:57481761-57481774 chr12:57481537-57481555 chr12:57482236-57482254 chr12:57481186-57481199
22	TAF1	chr12:57481492-57482561	A549	lung:	n/a	n/a
23	REST	chr12:57481537-57481917	PFSK-1	brain:	n/a	chr12:57481761-57481774 chr12:57481537-57481555
24	TAF1	chr12:57480573-57482679	ECC-1	luminal epithelium:	n/a	n/a
25	EP300	chr12:57481495-57481920	SK-N-SH_RA	brain:	n/a	n/a
26	SMARCB1	chr12:57480323-57482586	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:57481152-57481568	H1-hESC	embryonic stem cell:	n/a	n/a
28	EGR1	chr12:57480155-57483330	ECC-1	luminal epithelium:	n/a	chr12:57482835-57482844 chr12:57480431-57480445 chr12:57481121-57481131 chr12:57481095-57481108 chr12:57482833-57482844 chr12:57481707-57481721 chr12:57482832-57482845 chr12:57482519-57482530 chr12:57481115-57481137 chr12:57481119-57481132 chr12:57481148-57481161 chr12:57482518-57482531 chr12:57480458-57480472 chr12:57481121-57481130 chr12:57482835-57482845 chr12:57482567-57482577 chr12:57481228-57481238 chr12:57482834-57482844 chr12:57480458-57480469 chr12:57481120-57481131 chr12:57482832-57482846 chr12:57482520-57482530 chr12:57481079-57481089 chr12:57482518-57482531 chr12:57481627-57481640 chr12:57482519-57482533 chr12:57481619-57481629 chr12:57480503-57480516 chr12:57480313-57480323 chr12:57482520-57482530 chr12:57481118-57481133 chr12:57482878-57482888 chr12:57481122-57481131 chr12:57482834-57482844 chr12:57482832-57482845 chr12:57482441-57482454 chr12:57481120-57481131 chr12:57481681-57481691 chr12:57481119-57481132 chr12:57482832-57482845 chr12:57482518-57482532 chr12:57480457-57480470 chr12:57481229-57481239 chr12:57481121-57481131 chr12:57482828-57482850 chr12:57480503-57480516 chr12:57480311-57480321 chr12:57482838-57482851 chr12:57481119-57481133 chr12:57481119-57481132 chr12:57482831-57482846 chr12:57481017-57481031 chr12:57481119-57481132 chr12:57482832-57482845 chr12:57480456-57480471 chr12:57481243-57481256 chr12:57481503-57481527 chr12:57480832-57480845 chr12:57482519-57482530 chr12:57482521-57482530
29	STAT3	chr12:57480298-57481916	MCF10A-Er-Src	breast:	n/a	chr12:57481682-57481694 chr12:57481081-57481093 chr12:57480409-57480417 chr12:57481161-57481173 chr12:57480933-57480945 chr12:57480890-57480902 chr12:57481160-57481172 chr12:57480307-57480319 chr12:57480309-57480321 chr12:57481634-57481646 chr12:57481231-57481243 chr12:57481831-57481838 chr12:57481560-57481572
30	EP300	chr12:57481505-57481924	SK-N-SH_RA	brain:	n/a	n/a
31	MXI1	chr12:57480250-57483091	GM12878	blood:	n/a	chr12:57481172-57481181
32	TAF1	chr12:57480777-57482038	GM12878	blood:	n/a	n/a
33	RUNX3	chr12:57479937-57482985	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:57480514-57482578	GM12891	blood:	n/a	n/a
35	NR2F2	chr12:57481536-57482669	K562	blood:	n/a	n/a
36	EP300	chr12:57481418-57482685	A549	lung:	n/a	chr12:57481959-57481969
37	POLR2A	chr12:57481269-57482589	K562	blood:	n/a	n/a
38	BACH1	chr12:57480672-57482594	H1-hESC	embryonic stem cell:	n/a	n/a
39	PAX5	chr12:57480807-57481793	GM12892	blood:	n/a	chr12:57480860-57480869
40	CHD2	chr12:57480787-57483232	Hela-S3	cervix:	n/a	chr12:57481233-57481243 chr12:57480976-57480986
41	POLR2A	chr12:57481473-57482070	HUVEC	blood vessel:	n/a	n/a
42	RCOR1	chr12:57479770-57482970	K562	blood:	n/a	n/a
43	GATA3	chr12:57480747-57482842	A549	lung:	n/a	n/a
44	POLR2A	chr12:57480847-57481651	A549	lung:	n/a	n/a
45	CEBPD	chr12:57481400-57481904	HepG2	liver:	n/a	n/a
46	RELA	chr12:57479988-57481946	GM19099	blood:	n/a	n/a
47	ZEB1	chr12:57481374-57482033	GM12878	blood:	n/a	chr12:57481592-57481599
48	MAX	chr12:57480765-57483350	MCF-7	breast:	n/a	chr12:57481172-57481182 chr12:57482476-57482487 chr12:57482875-57482885 chr12:57481174-57481181 chr12:57481781-57481791 chr12:57481093-57481103 chr12:57481834-57481842 chr12:57481164-57481174 chr12:57482520-57482529 chr12:57481680-57481690 chr12:57481172-57481183 chr12:57483153-57483163
49	POLR2A	chr12:57479875-57482601	MCF10A-Er-Src	breast:	n/a	n/a
50	ATF2	chr12:57481502-57482612	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57481089..57481593-chr3:155588853..155589555,2	Hela-S3	cervix:
2	chr12:57480730..57482980-chr22:30821436..30824082,2	MCF-7	breast:
3	chr12:57398945..57400725-chr12:57479656..57482846,3	MCF-7	breast:
4	chr12:57480746..57483234-chr12:57915069..57916762,2	MCF-7	breast:
5	chr12:57480385..57481956-chr17:27071782..27073912,2	MCF-7	breast:
6	chr12:57480720..57482842-chr12:58137848..58140572,2	MCF-7	breast:
7	chr12:57480170..57482164-chr12:57622267..57624511,2	MCF-7	breast:
8	chr12:57118003..57119898-chr12:57480309..57484526,4	K562	blood:
9	chr12:57422175..57424146-chr12:57481515..57483170,2	MCF-7	breast:
10	chr12:57022390..57024526-chr12:57480119..57483489,4	MCF-7	breast:
11	chr12:57481154..57481806-chr3:5024696..5025683,2	Hela-S3	cervix:
12	chr12:57480017..57482545-chr14:24683866..24686216,2	MCF-7	breast:
13	chr12:57349108..57350665-chr12:57479276..57481586,2	MCF-7	breast:
14	chr12:57480163..57481794-chr12:57559962..57562744,2	MCF-7	breast:
15	chr12:57451485..57454907-chr12:57478514..57481800,3	MCF-7	breast:
16	chr12:57478864..57481857-chr15:89876636..89879186,2	MCF-7	breast:
17	chr12:57118215..57120672-chr12:57479913..57482298,4	K562	blood:
18	chr12:57478737..57483929-chr12:57633097..57638164,8	MCF-7	breast:
19	chr12:57481298..57482246-chr15:91497664..91498506,2	Hela-S3	cervix:
20	chr12:57479977..57484073-chr12:57519609..57523791,10	MCF-7	breast:
21	chr12:57116631..57120456-chr12:57479265..57482503,6	MCF-7	breast:
22	chr12:57481012..57482707-chr3:64002867..64005175,2	MCF-7	breast:
23	chr12:57385703..57388264-chr12:57481294..57482820,2	K562	blood:
24	chr12:57144616..57146221-chr12:57481056..57483916,2	K562	blood:
25	chr12:57480700..57481681-chr15:60771108..60771719,2	Hela-S3	cervix:
26	chr1:26361762..26362643-chr12:57481006..57481634,2	NB4	blood:
27	chr12:57480031..57482599-chr12:58144777..58147375,2	MCF-7	breast:
28	chr12:57479708..57482398-chr6:26204786..26207325,2	MCF-7	breast:
29	chr12:57480620..57481589-chr2:88315529..88316290,2	Hela-S3	cervix:
30	chr12:57143195..57148502-chr12:57480974..57485182,5	K562	blood:
31	chr12:56511049..56513507-chr12:57480483..57482738,2	MCF-7	breast:
32	chr12:57481329..57482067-chr17:7387451..7388155,2	Hela-S3	cervix:
33	chr12:57026457..57031197-chr12:57479410..57483153,5	MCF-7	breast:
34	chr12:57080529..57082220-chr12:57480203..57482961,2	MCF-7	breast:
35	chr12:57480840..57481798-chr20:52209705..52210327,2	Hela-S3	cervix:
36	chr12:57471513..57472336-chr12:57480807..57481598,2	Hela-S3	cervix:
37	chr12:57481135..57482003-chr5:10249503..10250543,3	Hela-S3	cervix:
38	chr12:57481073..57481737-chr16:2204976..2205651,2	Hela-S3	cervix:
39	chr12:57028665..57030374-chr12:57480509..57482064,2	K562	blood:
40	chr12:57480767..57481736-chr3:127843064..127843790,2	Hela-S3	cervix:
41	chr12:21654617..21655263-chr12:57481242..57482048,2	Hela-S3	cervix:
42	chr12:57117875..57121156-chr12:57480482..57484573,7	MCF-7	breast:
43	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:
44	chr12:57480219..57483297-chr12:57622863..57624907,4	MCF-7	breast:
45	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
NAB2	TF binding region
ENSG00000260669	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000150756	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000076604	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000166856	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000150753	Chromatin interaction
ENSG00000182199	Chromatin interaction
ENSG00000166965	Chromatin interaction
ENSG00000111711	Chromatin interaction
ENSG00000140521	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000166860	Chromatin interaction
ENSG00000258384	Chromatin interaction
ENSG00000166863	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000261441	Chromatin interaction
ENSG00000135446	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	chr12:57479800-57482400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
2	chr12:57480000-57481600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:57480000-57481800	Active TSS	Brain Angular Gyrus	brain
4	chr12:57480000-57483800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:57480000-57484000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr12:57480000-57484400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:57480000-57484400	Active TSS	Aorta	Aorta
8	chr12:57480000-57484400	Active TSS	Left Ventricle	heart
9	chr12:57480000-57484400	Active TSS	Right Atrium	heart
10	chr12:57480000-57485200	Active TSS	Psoas Muscle	Psoas
11	chr12:57480200-57481600	Active TSS	Fetal Brain Female	brain
12	chr12:57480200-57481800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:57480200-57481800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:57480200-57481800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:57480200-57482000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:57480200-57482400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr12:57480200-57482400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:57480200-57483800	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr12:57480200-57484000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:57480200-57484000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:57480200-57484000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:57480200-57484000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:57480200-57484400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:57480200-57484400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:57480200-57484400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:57480200-57484400	Active TSS	Brain Anterior Caudate	brain
27	chr12:57480200-57484400	Active TSS	Lung	lung
28	chr12:57480200-57484600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:57480400-57481600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:57480400-57481600	Active TSS	Stomach Smooth Muscle	stomach
31	chr12:57480400-57481800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:57480400-57481800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:57480400-57481800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:57480400-57481800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:57480400-57481800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:57480400-57481800	Active TSS	Liver	Liver
37	chr12:57480400-57481800	Active TSS	Duodenum Mucosa	Duodenum
38	chr12:57480400-57481800	Active TSS	Pancreas	Pancrea
39	chr12:57480400-57481800	Active TSS	GM12878-XiMat	blood
40	chr12:57480400-57481800	Active TSS	Hela-S3	cervix
41	chr12:57480400-57481800	Active TSS	HSMM	muscle
42	chr12:57480400-57481800	Active TSS	HSMMtube	muscle
43	chr12:57480400-57481800	Active TSS	K562	blood
44	chr12:57480400-57481800	Active TSS	NH-A	brain
45	chr12:57480400-57481800	Active TSS	NHDF-Ad	bronchial
46	chr12:57480400-57481800	Active TSS	NHLF	lung
47	chr12:57480400-57482000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr12:57480400-57482000	Active TSS	Brain Hippocampus Middle	brain
49	chr12:57480400-57482000	Active TSS	Placenta Amnion	Placenta Amnion
50	chr12:57480400-57483600	Active TSS	Spleen	Spleen

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