Variant report

Variant	rs62097858
Chromosome Location	chr18:12862581-12862582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr18:12862457-12862775	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOS	chr18:12862509-12863032	MCF10A-Er-Src	breast:	n/a	n/a
3	TEAD4	chr18:12862494-12862968	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr18:12862398-12862825	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr18:12862515-12862853	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUN	chr18:12862489-12862915	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBP	chr18:12862426-12862750	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr18:12862554-12862682	ProgFib	skin:	n/a	n/a
9	MAFF	chr18:12862527-12862755	HepG2	liver:	n/a	n/a
10	BACH1	chr18:12862468-12862826	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr18:12862329-12862877	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr18:12862479-12862792	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr18:12862322-12862586	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr18:12862371-12862951	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFK	chr18:12862512-12862694	HepG2	liver:	n/a	n/a
16	STAT3	chr18:12862517-12862950	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr18:12862494-12863029	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr18:12862380-12862816	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUND	chr18:12862450-12863023	H1-hESC	embryonic stem cell:	n/a	chr18:12862467-12862479
20	TEAD4	chr18:12862446-12862895	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12862494..12865307-chr18:12880258..12883236,3	MCF-7	breast:

No data

Variant related genes	Relation type
PTPN2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10502416	0.90[ASN][1000 genomes]
rs11080605	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11080606	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16939910	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3737361	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3786158	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55982017	0.81[ASN][1000 genomes]
rs56150366	0.83[ASN][1000 genomes]
rs62097819	0.94[ASN][1000 genomes]
rs62097820	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7227207	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7242788	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7244152	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8091720	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
2	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
4	chr18:12839600-12862600	Weak transcription	HSMM	muscle
5	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
6	chr18:12841000-12863200	Weak transcription	Colonic Mucosa	Colon
7	chr18:12841400-12863400	Weak transcription	Esophagus	oesophagus
8	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr18:12844400-12862600	Weak transcription	K562	blood
10	chr18:12847200-12862600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr18:12849000-12862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:12852000-12863200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr18:12852400-12862600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:12852400-12862600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr18:12852400-12863000	Weak transcription	NHLF	lung
16	chr18:12854800-12864000	Weak transcription	Brain Substantia Nigra	brain
17	chr18:12856400-12862800	Weak transcription	Osteobl	bone
18	chr18:12856600-12862800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr18:12856600-12863000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr18:12856600-12863400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr18:12856600-12863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr18:12856600-12863600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr18:12857000-12863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:12857400-12862600	Weak transcription	Lung	lung
25	chr18:12857400-12863000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr18:12857400-12863600	Weak transcription	Aorta	Aorta
27	chr18:12857400-12863800	Enhancers	Fetal Thymus	thymus
28	chr18:12857400-12872000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr18:12857600-12862600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr18:12857800-12862600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr18:12857800-12862600	Weak transcription	Spleen	Spleen
32	chr18:12857800-12863000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr18:12857800-12866200	Weak transcription	HSMMtube	muscle
34	chr18:12857800-12867600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr18:12857800-12881600	Weak transcription	Fetal Stomach	stomach
36	chr18:12858000-12872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:12858400-12862600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr18:12858400-12862600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:12858400-12862800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr18:12858400-12862800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr18:12858600-12867400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr18:12859600-12862600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr18:12859600-12862800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr18:12859600-12867000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr18:12859600-12876800	Weak transcription	Primary T cells from cord blood	blood
46	chr18:12859800-12862800	Weak transcription	HepG2	liver
47	chr18:12859800-12866600	Enhancers	Dnd41	blood
48	chr18:12860000-12862600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr18:12860200-12862600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr18:12860400-12863800	Enhancers	Primary B cells from peripheral blood	blood

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