Variant report

Variant	rs34799913
Chromosome Location	chr18:12863840-12863841
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	EP300	chr18:12863484-12864201	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr18:12863527-12864094	SK-N-SH_RA	brain:	n/a	n/a
3	FOS	chr18:12863762-12864044	MCF10A-Er-Src	breast:	n/a	chr18:12863875-12863885 chr18:12863876-12863884 chr18:12863875-12863885 chr18:12863892-12863904

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

Variant related genes	Relation type
PTPN2	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12955302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963474	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12964314	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12968719	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12969241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34153303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34416003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35320197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35923716	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35954636	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35967540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353227	0.90[EUR][1000 genomes];0.85[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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
2	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr18:12854800-12864000	Weak transcription	Brain Substantia Nigra	brain
4	chr18:12857400-12872000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:12857800-12866200	Weak transcription	HSMMtube	muscle
6	chr18:12857800-12867600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr18:12857800-12881600	Weak transcription	Fetal Stomach	stomach
8	chr18:12858000-12872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:12858600-12867400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr18:12859600-12867000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr18:12859600-12876800	Weak transcription	Primary T cells from cord blood	blood
12	chr18:12859800-12866600	Enhancers	Dnd41	blood
13	chr18:12861000-12864000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr18:12861000-12864400	Enhancers	Primary B cells from cord blood	blood
15	chr18:12861400-12865200	Enhancers	Fetal Lung	lung
16	chr18:12861600-12865000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr18:12861800-12870000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr18:12861800-12872600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr18:12862200-12865800	Enhancers	Pancreas	Pancrea
20	chr18:12862400-12864400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr18:12862400-12864600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr18:12862800-12877000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr18:12863000-12864000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr18:12863000-12864400	Enhancers	NHLF	lung
25	chr18:12863000-12865000	Weak transcription	K562	blood
26	chr18:12863000-12872200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr18:12863000-12879000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr18:12863000-12879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr18:12863200-12865000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr18:12863200-12867800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:12863200-12879000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr18:12863200-12879800	Weak transcription	Hela-S3	cervix
33	chr18:12863200-12880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr18:12863400-12864400	Weak transcription	Lung	lung
35	chr18:12863400-12868200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr18:12863400-12872400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr18:12863400-12875400	Weak transcription	HepG2	liver
38	chr18:12863400-12875800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:12863400-12879200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr18:12863400-12879800	Weak transcription	NHEK	skin
41	chr18:12863400-12881400	Weak transcription	Right Atrium	heart
42	chr18:12863600-12865200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr18:12863600-12872000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr18:12863600-12872200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr18:12863600-12875600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr18:12863600-12876200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr18:12863600-12880000	Weak transcription	Esophagus	oesophagus
48	chr18:12863600-12882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr18:12863800-12864000	Enhancers	Brain Anterior Caudate	brain
50	chr18:12863800-12864200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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