Variant report

Variant	rs13292865
Chromosome Location	chr9:8486482-8486483
allele	C/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	RAD21	chr9:8486011-8486503	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr9:8485876-8486619	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr9:8485934-8486484	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr9:8486038-8486545	SK-N-SH	brain:	n/a	n/a
5	MAX	chr9:8486200-8486498	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr9:8486194-8486534	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr9:8486011-8486495	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr9:8486360-8486510	HFF	foreskin:	n/a	n/a
9	MAX	chr9:8486201-8486506	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PTPRD	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10115201	0.86[EUR][1000 genomes]
rs10115554	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10116020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10124277	0.86[EUR][1000 genomes]
rs1323592	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13286908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13290896	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs13294270	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs13296910	0.88[JPT][hapmap]
rs13298803	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs13301979	0.85[ASN][1000 genomes]
rs16928002	1.00[CEU][hapmap]
rs16928048	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16928053	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs16928058	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2296102	1.00[CEU][hapmap]
rs34190427	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34599557	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35441574	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35777094	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35929428	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4338166	0.83[AMR][1000 genomes]
rs4409447	0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs4495488	0.88[JPT][hapmap]
rs4549838	0.81[AMR][1000 genomes]
rs62534023	0.83[AMR][1000 genomes]
rs62534039	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62534040	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7863060	0.92[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv892229	chr9:8485201-8520366	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
3	chr9:8442200-8522200	Weak transcription	Liver	Liver
4	chr9:8448000-8494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
6	chr9:8464600-8494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:8473600-8491600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:8476800-8491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:8477000-8491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:8478000-8487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:8478400-8488800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:8479000-8491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
16	chr9:8481600-8488200	Strong transcription	Fetal Lung	lung
17	chr9:8482200-8487000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:8482400-8491800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:8483800-8486600	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr9:8483800-8487000	Strong transcription	Dnd41	blood
21	chr9:8483800-8524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:8484400-8492000	Weak transcription	Fetal Stomach	stomach
23	chr9:8484400-8492800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:8484400-8492800	Weak transcription	Brain Substantia Nigra	brain
25	chr9:8484800-8487000	Strong transcription	Brain Germinal Matrix	brain
26	chr9:8485000-8488800	Strong transcription	Fetal Brain Female	brain
27	chr9:8486000-8491600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:8486000-8491600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:8486000-8491800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:8486000-8493800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:8486000-8495000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:8486000-8508400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:8486000-8519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:8486000-8522200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:8486200-8491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:8486200-8492000	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:8486200-8492800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:8486200-8501800	Weak transcription	Fetal Heart	heart
39	chr9:8486200-8504600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:8486200-8509000	Weak transcription	Brain Anterior Caudate	brain
41	chr9:8486200-8517200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr9:8486200-8522800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:8486200-8523200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
45	chr9:8486400-8489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:8486400-8489400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:8486400-8492000	Weak transcription	Fetal Brain Male	brain
48	chr9:8486400-8494000	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:8486400-8494400	Weak transcription	Brain Angular Gyrus	brain
50	chr9:8486400-8494400	Weak transcription	Ovary	ovary

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