Variant report

Variant	rs2233267
Chromosome Location	chr12:57482264-57482265
allele	A/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	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
13	HEY1	chr12:57480273-57482609	K562	blood:	n/a	chr12:57480500-57480515
14	POLR2A	chr12:57482156-57483151	H1-neurons	neurons:	n/a	n/a
15	SIN3AK20	chr12:57482182-57482544	PFSK-1	brain:	n/a	n/a
16	BCLAF1	chr12:57481625-57482613	GM12878	blood:	n/a	chr12:57481821-57481830 chr12:57482546-57482559
17	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
18	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
19	EP300	chr12:57482150-57482856	MCF-7	breast:	n/a	n/a
20	HDAC2	chr12:57481421-57482706	HepG2	liver:	n/a	n/a
21	TAF1	chr12:57482191-57482515	GM12891	blood:	n/a	n/a
22	EP300	chr12:57481477-57483142	MCF-7	breast:	n/a	chr12:57482999-57483015 chr12:57481959-57481969
23	ETS1	chr12:57481847-57482622	A549	lung:	n/a	chr12:57482505-57482522 chr12:57482546-57482557 chr12:57482505-57482522
24	NFIC	chr12:57482249-57482626	HepG2	liver:	n/a	n/a
25	E2F6	chr12:57482221-57482614	K562	blood:	n/a	chr12:57482546-57482555 chr12:57482465-57482474 chr12:57482491-57482506
26	POLR2A	chr12:57479540-57482719	GM12878	blood:	n/a	n/a
27	BCL3	chr12:57482139-57482615	GM12878	blood:	n/a	chr12:57482546-57482559
28	ZKSCAN1	chr12:57481361-57482576	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr12:57482214-57482610	HepG2	liver:	n/a	n/a
30	CEBPB	chr12:57482080-57482609	K562	blood:	n/a	n/a
31	MYC	chr12:57482248-57482461	GM12878	blood:	n/a	n/a
32	USF1	chr12:57482150-57482623	A549	lung:	n/a	n/a
33	TCF7L2	chr12:57481721-57482519	Hela-S3	cervix:	n/a	n/a
34	USF1	chr12:57482143-57482723	SK-N-SH	brain:	n/a	n/a
35	FOXA1	chr12:57482138-57482622	HepG2	liver:	n/a	n/a
36	E2F6	chr12:57481907-57482663	A549	lung:	n/a	chr12:57482546-57482555 chr12:57482465-57482474 chr12:57482491-57482506
37	POLR2A	chr12:57481165-57482591	GM12891	blood:	n/a	n/a
38	REST	chr12:57481181-57482609	A549	lung:	n/a	chr12:57481761-57481774 chr12:57481537-57481555 chr12:57482236-57482254 chr12:57481186-57481199
39	TAF1	chr12:57481492-57482561	A549	lung:	n/a	n/a
40	FOXP2	chr12:57482236-57482554	SK-N-MC	brain:	n/a	n/a
41	SIN3AK20	chr12:57482169-57482656	K562	blood:	n/a	n/a
42	BHLHE40	chr12:57481905-57482948	HepG2	liver:	n/a	n/a
43	CEBPB	chr12:57482158-57482625	HepG2	liver:	n/a	n/a
44	TAF1	chr12:57480573-57482679	ECC-1	luminal epithelium:	n/a	n/a
45	FOXA2	chr12:57481662-57482681	A549	lung:	n/a	n/a
46	KAP1	chr12:57481787-57482514	U2OS	brain:	n/a	n/a
47	SMARCB1	chr12:57480323-57482586	Hela-S3	cervix:	n/a	n/a
48	PAX5	chr12:57482214-57482632	GM12878	blood:	n/a	n/a
49	MAFK	chr12:57482185-57482458	HepG2	liver:	n/a	n/a
50	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

No.	Distal block	Cell Line	Cell type
1	chr10:73975137..73976051-chr12:57481746..57482269,2	NB4	blood:
2	chr12:57480730..57482980-chr22:30821436..30824082,2	MCF-7	breast:
3	chr11:61583939..61584830-chr12:57481915..57482436,2	Hela-S3	cervix:
4	chr12:57398945..57400725-chr12:57479656..57482846,3	MCF-7	breast:
5	chr12:57481772..57482283-chr6:26156284..26157226,2	Hela-S3	cervix:
6	chr12:56473732..56475652-chr12:57482023..57483860,2	MCF-7	breast:
7	chr1:161284102..161284624-chr12:57481715..57482320,2	NB4	blood:
8	chr12:57480746..57483234-chr12:57915069..57916762,2	MCF-7	breast:
9	chr12:57143938..57146732-chr12:57482240..57484256,2	MCF-7	breast:
10	chr12:57480720..57482842-chr12:58137848..58140572,2	MCF-7	breast:
11	chr12:57118003..57119898-chr12:57480309..57484526,4	K562	blood:
12	chr12:57422175..57424146-chr12:57481515..57483170,2	MCF-7	breast:
13	chr12:57022390..57024526-chr12:57480119..57483489,4	MCF-7	breast:
14	chr12:57480017..57482545-chr14:24683866..24686216,2	MCF-7	breast:
15	chr11:126173346..126174012-chr12:57481744..57482542,2	Hela-S3	cervix:
16	chr12:57118215..57120672-chr12:57479913..57482298,4	K562	blood:
17	chr12:57478737..57483929-chr12:57633097..57638164,8	MCF-7	breast:
18	chr12:57479977..57484073-chr12:57519609..57523791,10	MCF-7	breast:
19	chr12:57116631..57120456-chr12:57479265..57482503,6	MCF-7	breast:
20	chr12:57481012..57482707-chr3:64002867..64005175,2	MCF-7	breast:
21	chr12:57385703..57388264-chr12:57481294..57482820,2	K562	blood:
22	chr12:57144616..57146221-chr12:57481056..57483916,2	K562	blood:
23	chr12:57481564..57482544-chr17:8076551..8077091,2	Hela-S3	cervix:
24	chr12:57480031..57482599-chr12:58144777..58147375,2	MCF-7	breast:
25	chr12:57479708..57482398-chr6:26204786..26207325,2	MCF-7	breast:
26	chr12:57143195..57148502-chr12:57480974..57485182,5	K562	blood:
27	chr12:56511049..56513507-chr12:57480483..57482738,2	MCF-7	breast:
28	chr12:57481885..57482424-chr20:30192684..30193542,2	Hela-S3	cervix:
29	chr12:57026457..57031197-chr12:57479410..57483153,5	MCF-7	breast:
30	chr12:57080529..57082220-chr12:57480203..57482961,2	MCF-7	breast:
31	chr12:57481778..57482507-chr3:119812302..119813196,2	Hela-S3	cervix:
32	chr12:57117875..57121156-chr12:57480482..57484573,7	MCF-7	breast:
33	chr12:57481808..57482426-chr6:116574885..116575616,2	HCT-116	colon:
34	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:
35	chr12:57480219..57483297-chr12:57622863..57624907,4	MCF-7	breast:
36	chr12:57482175..57482736-chr19:39897077..39898067,2	Hela-S3	cervix:
37	chr12:57481972..57484968-chr12:57912943..57915711,3	K562	blood:
38	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
TMEM194A	TF binding region
ENSG00000196531	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000182199	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000111817	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000166295	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000166856	Chromatin interaction
ENSG00000166863	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000166860	Chromatin interaction
ENSG00000149485	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000260669	Chromatin interaction
ENSG00000110063	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000138303	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000134824	Chromatin interaction
ENSG00000143252	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000237021	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000187189	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000198056	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1044939	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10506351	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1552245	0.80[ASN][1000 genomes]
rs17119344	0.82[ASN][1000 genomes]
rs17119352	0.80[ASN][1000 genomes]
rs17119386	0.81[ASN][1000 genomes]
rs17119388	0.81[ASN][1000 genomes]
rs17119390	0.82[ASN][1000 genomes]
rs17119407	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17119416	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17119418	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2035545	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270736	0.82[ASN][1000 genomes]
rs2270737	0.80[ASN][1000 genomes]
rs2270739	0.81[ASN][1000 genomes]
rs3024974	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3024975	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34762603	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35937600	0.96[ASN][1000 genomes]
rs3759134	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759135	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782329	0.81[ASN][1000 genomes]
rs3782330	0.81[ASN][1000 genomes]
rs4039	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4143085	0.81[ASN][1000 genomes]
rs56128678	0.82[ASN][1000 genomes]
rs56270558	0.82[ASN][1000 genomes]
rs56354404	0.82[ASN][1000 genomes]
rs57056392	0.81[ASN][1000 genomes]
rs58389529	0.80[ASN][1000 genomes]
rs61504157	0.81[ASN][1000 genomes]
rs66741626	0.99[ASN][1000 genomes]
rs7135297	0.86[ASN][1000 genomes]
rs7298475	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73114437	0.80[ASN][1000 genomes]
rs73114446	0.80[ASN][1000 genomes]
rs73114452	0.80[ASN][1000 genomes]
rs73114457	0.82[ASN][1000 genomes]
rs73114459	0.82[ASN][1000 genomes]
rs73114467	0.82[ASN][1000 genomes]
rs73114468	0.82[ASN][1000 genomes]
rs73114472	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73116494	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73116501	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73118413	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73118416	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73118418	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73118432	0.93[EUR][1000 genomes]
rs755221	0.82[ASN][1000 genomes]
rs7961920	0.81[ASN][1000 genomes]
rs7962771	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]

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	chr12:57480000-57483800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:57480000-57484000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:57480000-57484400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:57480000-57484400	Active TSS	Aorta	Aorta
6	chr12:57480000-57484400	Active TSS	Left Ventricle	heart
7	chr12:57480000-57484400	Active TSS	Right Atrium	heart
8	chr12:57480000-57485200	Active TSS	Psoas Muscle	Psoas
9	chr12:57480200-57482400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr12:57480200-57482400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:57480200-57483800	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr12:57480200-57484000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:57480200-57484000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:57480200-57484000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr12:57480200-57484000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:57480200-57484400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr12:57480200-57484400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:57480200-57484400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:57480200-57484400	Active TSS	Brain Anterior Caudate	brain
20	chr12:57480200-57484400	Active TSS	Lung	lung
21	chr12:57480200-57484600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:57480400-57483600	Active TSS	Spleen	Spleen
23	chr12:57480400-57483800	Active TSS	Brain Cingulate Gyrus	brain
24	chr12:57480400-57483800	Active TSS	Small Intestine	intestine
25	chr12:57480400-57484400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:57480400-57484400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:57480400-57484400	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:57480400-57484400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:57480400-57484400	Active TSS	Esophagus	oesophagus
30	chr12:57480400-57484400	Active TSS	Right Ventricle	heart
31	chr12:57480400-57484600	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr12:57480400-57485000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:57480600-57483600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:57480600-57483800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:57480600-57484000	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:57480600-57484200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:57480600-57484400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:57480600-57484400	Active TSS	Colon Smooth Muscle	Colon
39	chr12:57480600-57484400	Active TSS	Thymus	Thymus
40	chr12:57480600-57484600	Active TSS	Ovary	ovary
41	chr12:57480800-57483600	Active TSS	Fetal Stomach	stomach
42	chr12:57480800-57483800	Active TSS	Gastric	stomach
43	chr12:57480800-57484800	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr12:57480800-57485000	Active TSS	Fetal Kidney	kidney
45	chr12:57481200-57482400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr12:57481200-57482400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:57481200-57482400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:57481200-57482400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr12:57481200-57482600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr12:57481200-57482600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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