Variant report

Variant	rs1533246
Chromosome Location	chr12:124019055-124019056
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	PBX3	chr12:124018688-124019299	SK-N-SH	brain:	n/a	n/a
2	MAX	chr12:124017255-124019286	HepG2	liver:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
3	POLR2A	chr12:124017557-124019155	K562	blood:	n/a	n/a
4	MXI1	chr12:124018345-124019113	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:124017306-124019150	HepG2	liver:	n/a	n/a
6	CTCF	chr12:124018272-124019282	A549	lung:	n/a	chr12:124018907-124018916
7	POLR2A	chr12:124017688-124019111	K562	blood:	n/a	n/a
8	MAX	chr12:124017326-124019119	K562	blood:	n/a	chr12:124017624-124017639
9	POLR2A	chr12:124018902-124019101	Hela-S3	cervix:	n/a	n/a
10	USF2	chr12:124018929-124019093	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:124017562-124019144	HUVEC	blood vessel:	n/a	n/a
12	ZBTB7A	chr12:124018326-124019309	ECC-1	luminal epithelium:	n/a	chr12:124018617-124018625
13	SIN3AK20	chr12:124018779-124019122	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:124018305-124019111	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr12:124017269-124019274	A549	lung:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
16	CTCF	chr12:124018960-124019110	NHDF-neo	bronchial:	n/a	n/a
17	SIN3A	chr12:124018847-124019139	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:124017727-124019089	K562	blood:	n/a	n/a
19	POLR2A	chr12:124018207-124019131	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr12:124018331-124019073	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr12:124018804-124019116	K562	blood:	n/a	n/a
22	CHD2	chr12:124018432-124019068	K562	blood:	n/a	chr12:124018515-124018525
23	TEAD4	chr12:124018892-124019237	H1-hESC	embryonic stem cell:	n/a	n/a
24	ZBTB7A	chr12:124018147-124019171	K562	blood:	n/a	chr12:124018617-124018625
25	ZBTB7A	chr12:124018335-124019056	K562	blood:	n/a	chr12:124018617-124018625
26	RFX5	chr12:124018410-124019109	Hela-S3	cervix:	n/a	n/a
27	MAZ	chr12:124016579-124019401	IMR90	lung:	n/a	chr12:124019137-124019147 chr12:124016824-124016835 chr12:124017249-124017259 chr12:124017624-124017639
28	POLR2A	chr12:124017644-124019078	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:124018029-124019143	HEK293	kidney:	n/a	n/a
30	CHD2	chr12:124018613-124019088	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr12:124018267-124019551	H1-neurons	neurons:	n/a	chr12:124018410-124018423 chr12:124019137-124019150
32	POLR2A	chr12:124018554-124019077	PANC-1	pancreas:	n/a	n/a
33	CTCF	chr12:124018319-124019173	SK-N-SH	brain:	n/a	chr12:124018907-124018916
34	POLR2A	chr12:124017515-124019142	A549	lung:	n/a	n/a
35	POLR2A	chr12:124018538-124019125	Gliobla	brain:	n/a	n/a
36	RCOR1	chr12:124018371-124019297	K562	blood:	n/a	n/a
37	UBTF	chr12:124017689-124019103	K562	blood:	n/a	n/a
38	MXI1	chr12:124017183-124019192	IMR90	lung:	n/a	n/a
39	ZNF263	chr12:124018692-124019212	HEK293-T-REx	kidney:	n/a	n/a
40	CTCF	chr12:124018920-124019070	GM06990	blood:	n/a	n/a
41	MYC	chr12:124017262-124019228	A549	lung:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
42	MAX	chr12:124018558-124019316	MCF-7	breast:	n/a	chr12:124019137-124019147
43	MAZ	chr12:124017507-124019189	K562	blood:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
44	RCOR1	chr12:124018957-124019160	Hela-S3	cervix:	n/a	n/a
45	HMGN3	chr12:124017509-124019090	K562	blood:	n/a	n/a
46	ZBTB7A	chr12:124018463-124019319	ECC-1	luminal epithelium:	n/a	chr12:124018617-124018625
47	TCF12	chr12:124018586-124019337	A549	lung:	n/a	n/a
48	EP300	chr12:124018025-124019163	SK-N-SH	brain:	n/a	chr12:124018466-124018475 chr12:124018708-124018724
49	CTCF	chr12:124019000-124019150	GM12873	blood:	n/a	n/a
50	POLR2A	chr12:124017633-124019064	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:124018210..124020140-chr12:124067644..124069375,2	MCF-7	breast:
2	chr12:124018963..124020649-chr12:124025084..124027162,2	MCF-7	breast:
3	chr12:123997284..124000079-chr12:124017073..124019484,2	MCF-7	breast:
4	chr12:124018609..124020737-chr12:124028286..124031087,2	MCF-7	breast:
5	chr12:123921165..123922728-chr12:124019054..124020967,2	K562	blood:
6	chr12:123872416..123876102-chr12:124017252..124019601,4	MCF-7	breast:
7	chr12:123871385..123875741-chr12:124017374..124019532,6	MCF-7	breast:
8	chr12:124018289..124019128-chr19:50370267..50370907,2	Hela-S3	cervix:
9	chr12:124017816..124019657-chr12:124117596..124119161,2	MCF-7	breast:
10	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
11	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
12	chr12:123912338..123913868-chr12:124018894..124020678,2	K562	blood:
13	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
14	chr12:123948940..123951509-chr12:124017235..124019368,2	MCF-7	breast:
15	chr12:124018224..124020563-chr12:124065688..124070487,5	K562	blood:
16	chr12:123930108..123930636-chr12:124018341..124019216,2	MCF-7	breast:
17	chr12:124018351..124020362-chr12:124063140..124065356,2	MCF-7	breast:
18	chr12:124017444..124019100-chr12:124084646..124086674,2	MCF-7	breast:

Variant related genes	Relation type
RILPL1	TF binding region
MIR3908	TF binding region
ENSG00000150977	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000039650	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000266655	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2333832	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28492040	0.88[EUR][1000 genomes]
rs34734800	0.80[EUR][1000 genomes]
rs34944476	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35016092	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930717	0.82[EUR][1000 genomes]
rs61953540	0.80[EUR][1000 genomes]
rs61953541	0.80[EUR][1000 genomes]
rs6488877	0.85[EUR][1000 genomes]
rs6488878	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7303956	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7959714	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7963804	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3357232	chr12:124017349-124019447	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124016400-124019400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:124016800-124019200	Active TSS	Aorta	Aorta
3	chr12:124016800-124019400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:124016800-124019400	Active TSS	Right Atrium	heart
5	chr12:124017000-124019200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:124017000-124019200	Active TSS	Ovary	ovary
7	chr12:124017000-124019200	Active TSS	Psoas Muscle	Psoas
8	chr12:124017000-124019200	Active TSS	Right Ventricle	heart
9	chr12:124017000-124019200	Active TSS	NHLF	lung
10	chr12:124017000-124019400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:124017000-124019400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:124017000-124019600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:124017200-124019400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:124017200-124019400	Active TSS	Colon Smooth Muscle	Colon
15	chr12:124017200-124019400	Active TSS	HSMM	muscle
16	chr12:124017400-124019200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr12:124017400-124019200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr12:124017400-124019400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:124017400-124019400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:124017400-124019400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:124017400-124019400	Active TSS	Brain Angular Gyrus	brain
22	chr12:124017400-124019400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:124017400-124019400	Active TSS	Lung	lung
24	chr12:124017400-124019600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:124017600-124019200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:124017600-124019200	Active TSS	Brain Hippocampus Middle	brain
27	chr12:124017600-124019400	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:124017600-124019400	Active TSS	Hela-S3	cervix
29	chr12:124017600-124019600	Active TSS	Brain Anterior Caudate	brain
30	chr12:124017800-124019200	Active TSS	Brain Germinal Matrix	brain
31	chr12:124017800-124019200	Active TSS	Placenta Amnion	Placenta Amnion
32	chr12:124017800-124019400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:124017800-124019400	Active TSS	Fetal Brain Female	brain
34	chr12:124017800-124019400	Active TSS	HepG2	liver
35	chr12:124017800-124019400	Active TSS	HSMMtube	muscle
36	chr12:124017800-124019400	Active TSS	NH-A	brain
37	chr12:124018000-124019200	Active TSS	Primary T cells from cord blood	blood
38	chr12:124018000-124019200	Active TSS	Colonic Mucosa	Colon
39	chr12:124018000-124019200	Active TSS	Fetal Intestine Large	intestine
40	chr12:124018000-124019200	Active TSS	Gastric	stomach
41	chr12:124018000-124019200	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr12:124018000-124019200	Active TSS	Small Intestine	intestine
43	chr12:124018000-124019200	Bivalent/Poised TSS	Thymus	Thymus
44	chr12:124018000-124019400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr12:124018000-124019400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:124018000-124019400	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr12:124018000-124019600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:124018000-124019600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr12:124018600-124019200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr12:124018600-124019400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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