Variant report

Variant	rs1038291
Chromosome Location	chr4:87551840-87551841
allele	A/G
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	POLR2A	chr4:87551837-87552110	SK-N-SH	brain:	n/a	n/a
2	EP300	chr4:87551505-87552223	SK-N-SH	brain:	n/a	chr4:87551971-87551981
3	EP300	chr4:87551722-87552136	SK-N-SH_RA	brain:	n/a	chr4:87551971-87551981

Variant related genes	Relation type
PTPN13	TF binding region

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10029162	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097114	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1187208	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2086541	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2869441	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35084226	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4693770	0.82[CHB][hapmap]
rs6829466	0.86[CHB][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7660964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661663	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87531000-87553600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:87540400-87554000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:87540400-87556200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:87541200-87553400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:87541200-87571200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:87541600-87556200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:87542800-87557600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:87542800-87566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:87543000-87553200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87543200-87556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:87544200-87556000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:87544400-87556800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:87544400-87571200	Weak transcription	Pancreas	Pancrea
14	chr4:87546200-87569400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:87546400-87556400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:87546400-87557000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:87547000-87553600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:87547000-87556200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:87547600-87554400	Weak transcription	Fetal Kidney	kidney
20	chr4:87548000-87554000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:87548200-87553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:87548400-87553600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:87549000-87553200	Weak transcription	NHEK	skin
24	chr4:87549400-87553400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:87549400-87555600	Weak transcription	NHDF-Ad	bronchial
26	chr4:87550400-87552000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:87551000-87556200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:87551200-87552600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:87551200-87553400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:87551400-87556800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:87551800-87554800	Enhancers	Fetal Lung	lung

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