Variant report

Variant	rs10117452
Chromosome Location	chr9:8482971-8482972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10115800	1.00[MEX][hapmap]
rs10117929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10117964	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10119472	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10120463	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs10121790	1.00[MEX][hapmap]
rs10122545	0.83[AMR][1000 genomes]
rs10511495	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs10977126	0.83[AMR][1000 genomes]
rs10977134	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs10977136	1.00[MEX][hapmap];0.86[MKK][hapmap]
rs10977139	1.00[AMR][1000 genomes]
rs10977143	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10977145	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10977154	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs10977155	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10977166	1.00[MEX][hapmap]
rs12337324	1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[AMR][1000 genomes]
rs12340876	1.00[MEX][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12344148	1.00[MEX][hapmap]
rs12349550	1.00[MEX][hapmap]
rs12352210	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs16927991	0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28491557	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28588467	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56075951	0.86[AFR][1000 genomes]
rs56807533	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58706764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73640919	0.90[AFR][1000 genomes]
rs73640920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs745974	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9299065	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs9657635	0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][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	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

No data

Chromatin state (count:49 , 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	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
4	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8442200-8522200	Weak transcription	Liver	Liver
6	chr9:8448000-8494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
8	chr9:8464600-8494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:8465800-8484000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:8468600-8484000	Weak transcription	Ovary	ovary
11	chr9:8473200-8483400	Weak transcription	Fetal Stomach	stomach
12	chr9:8473600-8491600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:8474000-8484000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:8474400-8484800	Weak transcription	Fetal Heart	heart
15	chr9:8474400-8485200	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:8475400-8483400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:8475600-8483400	Weak transcription	Brain Substantia Nigra	brain
18	chr9:8476400-8483400	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:8476400-8483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:8476800-8491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:8477000-8491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:8477600-8485000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:8478000-8484000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:8478000-8487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:8478400-8488800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:8478800-8483800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:8478800-8485000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:8478800-8485800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:8479000-8491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:8479200-8483800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:8479400-8485200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:8480400-8483800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:8480400-8484000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:8480600-8483800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:8480600-8484000	Weak transcription	Brain Anterior Caudate	brain
38	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
39	chr9:8481600-8488200	Strong transcription	Fetal Lung	lung
40	chr9:8482200-8483000	Strong transcription	Brain Germinal Matrix	brain
41	chr9:8482200-8486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:8482200-8487000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:8482400-8491800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr9:8482600-8483000	Strong transcription	Dnd41	blood
45	chr9:8482600-8483400	Weak transcription	Fetal Brain Male	brain
46	chr9:8482600-8486000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:8482600-8486200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr9:8482800-8485000	Weak transcription	Fetal Brain Female	brain
49	chr9:8482800-8486200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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