Variant report

Variant	rs61637080
Chromosome Location	chr18:12839793-12839794
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	WRNIP1	chr18:12839120-12839936	GM12878	blood:	n/a	n/a
2	BCL11A	chr18:12839495-12840306	GM12878	blood:	n/a	n/a
3	EP300	chr18:12839005-12840207	GM12878	blood:	n/a	chr18:12839731-12839745
4	FOS	chr18:12839703-12840097	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr18:12839780-12839930	HCPEpiC	choroid plexus:	n/a	n/a
6	BHLHE40	chr18:12839024-12840191	GM12878	blood:	n/a	n/a
7	SPI1	chr18:12838997-12839893	HL-60	blood:	n/a	chr18:12839120-12839129
8	BATF	chr18:12839386-12840285	GM12878	blood:	n/a	chr18:12839866-12839875
9	POLR2A	chr18:12839006-12840079	GM12878	blood:	n/a	n/a
10	RCOR1	chr18:12839056-12840635	GM12878	blood:	n/a	n/a
11	STAT3	chr18:12839078-12840358	GM12878	blood:	n/a	chr18:12839120-12839131
12	SMC3	chr18:12839103-12840159	GM12878	blood:	n/a	n/a
13	CREB1	chr18:12838986-12840338	GM12878	blood:	n/a	n/a
14	SP1	chr18:12839639-12840055	GM12878	blood:	n/a	n/a
15	BCL11A	chr18:12839675-12840022	GM12878	blood:	n/a	n/a
16	RFX5	chr18:12839564-12840484	GM12878	blood:	n/a	n/a
17	MYC	chr18:12839666-12839984	MCF10A-Er-Src	breast:	n/a	n/a
18	TBL1XR1	chr18:12838992-12840681	GM12878	blood:	n/a	n/a
19	FOS	chr18:12838988-12840046	MCF10A-Er-Src	breast:	n/a	chr18:12839279-12839290 chr18:12839280-12839288
20	NFIC	chr18:12838267-12840405	GM12878	blood:	n/a	n/a
21	CHD2	chr18:12839074-12840351	GM12878	blood:	n/a	n/a
22	FOXM1	chr18:12838968-12840345	GM12878	blood:	n/a	n/a
23	NFATC1	chr18:12839491-12840333	GM12878	blood:	n/a	n/a
24	ATF2	chr18:12838993-12840431	GM12878	blood:	n/a	n/a
25	IRF4	chr18:12839580-12840104	GM12878	blood:	n/a	n/a
26	POLR2A	chr18:12837890-12839921	MCF10A-Er-Src	breast:	n/a	n/a
27	MTA3	chr18:12839028-12840352	GM12878	blood:	n/a	n/a
28	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
29	ZNF143	chr18:12839262-12840326	GM12878	blood:	n/a	n/a
30	POLR2A	chr18:12839070-12840021	GM12878	blood:	n/a	n/a
31	STAT1	chr18:12839197-12840232	GM12878	blood:	n/a	chr18:12839837-12839848
32	MAX	chr18:12839571-12839868	NB4	blood:	n/a	n/a
33	USF2	chr18:12839661-12840443	GM12878	blood:	n/a	n/a
34	EP300	chr18:12838996-12840925	GM12878	blood:	n/a	chr18:12840436-12840446 chr18:12839731-12839745
35	CUX1	chr18:12838518-12840492	GM12878	blood:	n/a	chr18:12839179-12839193
36	SP1	chr18:12839532-12840173	GM12878	blood:	n/a	n/a
37	FOS	chr18:12839701-12840041	MCF10A-Er-Src	breast:	n/a	n/a
38	EBF1	chr18:12839029-12840745	GM12878	blood:	n/a	n/a
39	MXI1	chr18:12838309-12840274	GM12878	blood:	n/a	chr18:12839264-12839279
40	BATF	chr18:12839544-12840340	GM12878	blood:	n/a	chr18:12839866-12839875
41	EP300	chr18:12839001-12840319	GM12878	blood:	n/a	chr18:12839731-12839745
42	POU2F2	chr18:12839026-12840078	GM12878	blood:	n/a	n/a
43	RUNX3	chr18:12838955-12840703	GM12878	blood:	n/a	n/a
44	BCLAF1	chr18:12839267-12840197	GM12878	blood:	n/a	n/a
45	POLR2A	chr18:12837093-12840014	MCF10A-Er-Src	breast:	n/a	n/a
46	MAZ	chr18:12839072-12840099	GM12878	blood:	n/a	n/a
47	PBX3	chr18:12839754-12839930	GM12878	blood:	n/a	n/a
48	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
49	IKZF1	chr18:12839140-12840535	GM12878	blood:	n/a	n/a
50	MAX	chr18:12839136-12840068	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12828774..12831402-chr18:12837889..12840391,3	K562	blood:
2	chr18:12836859..12842714-chr18:12880630..12885724,12	MCF-7	breast:
3	chr18:12838410..12841239-chr18:12848544..12850733,2	K562	blood:
4	chr18:12838530..12843294-chr18:12882526..12884530,4	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11080608	1.00[AMR][1000 genomes]
rs3809915	1.00[AMR][1000 genomes]
rs57095726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59520091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60267243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60287618	1.00[AMR][1000 genomes]
rs8087077	1.00[AMR][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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
3	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:12821000-12840400	Weak transcription	Brain Substantia Nigra	brain
5	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr18:12825400-12840400	Weak transcription	Spleen	Spleen
7	chr18:12827600-12843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:12828400-12842600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
10	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
11	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
12	chr18:12829200-12842200	Weak transcription	HUVEC	blood vessel
13	chr18:12829800-12841200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:12834200-12840400	Weak transcription	Lung	lung
15	chr18:12834200-12850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:12836200-12840200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:12836800-12842400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr18:12837400-12839800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr18:12837400-12840000	Enhancers	HMEC	breast
20	chr18:12837400-12841600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr18:12837600-12839800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr18:12837600-12839800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr18:12837600-12840400	Enhancers	Fetal Thymus	thymus
24	chr18:12838000-12841600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr18:12838200-12839800	Enhancers	K562	blood
26	chr18:12838200-12840200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr18:12838600-12840000	Enhancers	NHDF-Ad	bronchial
28	chr18:12838600-12840200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr18:12838600-12840200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr18:12838600-12840200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr18:12838600-12840200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr18:12838600-12840200	Enhancers	NHLF	lung
33	chr18:12838600-12840400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr18:12838600-12840400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr18:12838600-12840400	Enhancers	Liver	Liver
36	chr18:12838600-12840400	Weak transcription	Right Ventricle	heart
37	chr18:12838600-12840400	Enhancers	Osteobl	bone
38	chr18:12838600-12840600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr18:12838600-12840600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr18:12838600-12840800	Weak transcription	Fetal Muscle Leg	muscle
41	chr18:12838600-12841400	Enhancers	Pancreas	Pancrea
42	chr18:12838600-12841800	Weak transcription	Stomach Mucosa	stomach
43	chr18:12838600-12842200	Weak transcription	Placenta	Placenta
44	chr18:12838600-12842400	Weak transcription	Fetal Stomach	stomach
45	chr18:12838600-12843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr18:12838600-12843000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr18:12838600-12843000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr18:12838600-12843400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr18:12838600-12843400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr18:12838600-12843400	Weak transcription	Gastric	stomach

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