Variant report

Variant	rs16939910
Chromosome Location	chr18:12837993-12837994
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	STAT3	chr18:12837936-12838668	Hela-S3	cervix:	n/a	chr18:12838357-12838369 chr18:12838245-12838253 chr18:12838320-12838331 chr18:12838113-12838124
2	EP300	chr18:12837790-12838480	Hela-S3	cervix:	n/a	chr18:12838200-12838208
3	CEBPB	chr18:12837983-12838572	MCF-7	breast:	n/a	chr18:12838245-12838254 chr18:12838243-12838254 chr18:12838243-12838256
4	MYBL2	chr18:12837989-12838555	HepG2	liver:	n/a	n/a
5	POLR2A	chr18:12837890-12839921	MCF10A-Er-Src	breast:	n/a	n/a
6	SP1	chr18:12837989-12838702	A549	lung:	n/a	n/a
7	STAT3	chr18:12837844-12838515	MCF10A-Er-Src	breast:	n/a	chr18:12838357-12838369 chr18:12838245-12838253 chr18:12838320-12838331 chr18:12838113-12838124
8	FOSL2	chr18:12837895-12838512	A549	lung:	n/a	chr18:12838294-12838308
9	STAT3	chr18:12837596-12840175	MCF10A-Er-Src	breast:	n/a	chr18:12838357-12838369 chr18:12838245-12838253 chr18:12838320-12838331 chr18:12839120-12839131 chr18:12838113-12838124
10	FOXA2	chr18:12837754-12838820	A549	lung:	n/a	n/a
11	FOS	chr18:12837750-12838546	MCF10A-Er-Src	breast:	n/a	chr18:12838294-12838308
12	JUND	chr18:12837992-12838588	Hela-S3	cervix:	n/a	chr18:12838294-12838308
13	TBP	chr18:12837761-12838745	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr18:12837362-12838837	IMR90	lung:	n/a	n/a
15	FOS	chr18:12837747-12838620	MCF10A-Er-Src	breast:	n/a	chr18:12838294-12838308
16	CEBPB	chr18:12837771-12838686	Hela-S3	cervix:	n/a	chr18:12838245-12838254 chr18:12838243-12838254 chr18:12838243-12838256
17	EP300	chr18:12837923-12838421	K562	blood:	n/a	chr18:12838200-12838208
18	EP300	chr18:12837931-12838557	A549	lung:	n/a	chr18:12838200-12838208
19	POLR2A	chr18:12837093-12840014	MCF10A-Er-Src	breast:	n/a	n/a
20	TEAD4	chr18:12837935-12838554	HepG2	liver:	n/a	n/a
21	STAT3	chr18:12837651-12840143	MCF10A-Er-Src	breast:	n/a	chr18:12838357-12838369 chr18:12838245-12838253 chr18:12838320-12838331 chr18:12839120-12839131 chr18:12838113-12838124
22	TCF12	chr18:12837898-12838845	A549	lung:	n/a	n/a
23	CEBPB	chr18:12837871-12838684	HCT-116	colon:	n/a	chr18:12838245-12838254 chr18:12838243-12838254 chr18:12838243-12838256
24	FOS	chr18:12837730-12838638	MCF10A-Er-Src	breast:	n/a	chr18:12838294-12838308
25	GATA3	chr18:12837868-12838666	A549	lung:	n/a	chr18:12838461-12838472 chr18:12838376-12838386
26	STAT3	chr18:12837626-12840068	MCF10A-Er-Src	breast:	n/a	chr18:12838357-12838369 chr18:12838245-12838253 chr18:12838320-12838331 chr18:12839120-12839131 chr18:12838113-12838124
27	SP1	chr18:12837910-12838765	A549	lung:	n/a	n/a
28	SP1	chr18:12837951-12838678	HCT-116	colon:	n/a	n/a
29	EP300	chr18:12837894-12838720	A549	lung:	n/a	chr18:12838200-12838208
30	CEBPB	chr18:12837802-12838632	A549	lung:	n/a	chr18:12838245-12838254 chr18:12838243-12838254 chr18:12838243-12838256
31	MAZ	chr18:12837923-12838586	Hela-S3	cervix:	n/a	n/a
32	E2F4	chr18:12837700-12838466	MCF10A-Er-Src	breast:	n/a	n/a
33	MYC	chr18:12837642-12838709	MCF10A-Er-Src	breast:	n/a	n/a
34	BCL3	chr18:12837914-12838566	A549	lung:	n/a	n/a
35	CEBPB	chr18:12837975-12838587	ECC-1	luminal epithelium:	n/a	chr18:12838245-12838254 chr18:12838243-12838254 chr18:12838243-12838256

No.	Distal block	Cell Line	Cell type
1	chr18:12817654..12819738-chr18:12836432..12839410,2	K562	blood:
2	chr18:12828774..12831402-chr18:12837889..12840391,3	K562	blood:
3	chr18:12836738..12838821-chr18:12946925..12949352,2	K562	blood:
4	chr18:12836859..12842714-chr18:12880630..12885724,12	MCF-7	breast:

Variant related genes	Relation type
PTPN2	TF binding region
ENSG00000175354	Chromatin interaction
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10502416	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11080605	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11080606	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3737361	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786158	0.89[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56150366	0.82[ASN][1000 genomes]
rs62097819	0.94[ASN][1000 genomes]
rs62097820	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62097858	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7227207	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7242788	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7244152	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8091720	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
7	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
2	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
4	chr18:12809600-12838200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr18:12809600-12838200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:12812000-12838400	Weak transcription	Right Ventricle	heart
7	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:12820400-12838600	Weak transcription	Brain Angular Gyrus	brain
9	chr18:12820800-12838200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:12820800-12838200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:12821000-12840400	Weak transcription	Brain Substantia Nigra	brain
12	chr18:12821600-12839200	Weak transcription	Brain Anterior Caudate	brain
13	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr18:12825400-12838200	Weak transcription	Gastric	stomach
15	chr18:12825400-12840400	Weak transcription	Spleen	Spleen
16	chr18:12825600-12838200	Weak transcription	Aorta	Aorta
17	chr18:12825600-12838200	Weak transcription	K562	blood
18	chr18:12826000-12838400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr18:12826800-12838200	Weak transcription	Pancreas	Pancrea
20	chr18:12827600-12838200	Weak transcription	Esophagus	oesophagus
21	chr18:12827600-12838200	Weak transcription	Small Intestine	intestine
22	chr18:12827600-12838400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12827600-12843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr18:12828400-12842600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
26	chr18:12828800-12838200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:12828800-12838200	Weak transcription	Psoas Muscle	Psoas
28	chr18:12829000-12838200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr18:12829000-12839200	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
31	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
32	chr18:12829200-12842200	Weak transcription	HUVEC	blood vessel
33	chr18:12829400-12838200	Weak transcription	Stomach Mucosa	stomach
34	chr18:12829600-12838400	Weak transcription	Ovary	ovary
35	chr18:12829800-12841200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr18:12833800-12838200	Weak transcription	Colon Smooth Muscle	Colon
37	chr18:12834000-12838200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr18:12834000-12838200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr18:12834000-12838200	Weak transcription	Left Ventricle	heart
40	chr18:12834200-12838200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr18:12834200-12840400	Weak transcription	Lung	lung
42	chr18:12834200-12850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr18:12834400-12838200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr18:12834600-12838200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr18:12835000-12838000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr18:12835000-12838200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr18:12835000-12838200	Weak transcription	Fetal Stomach	stomach
48	chr18:12835200-12838200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr18:12836000-12838200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr18:12836200-12838200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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