Variant report

Variant	rs10117986
Chromosome Location	chr9:8482408-8482409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10114195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114412	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10119236	0.84[TSI][hapmap]
rs10125682	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10511497	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10511498	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758976	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10758977	0.92[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs10815885	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10815886	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10815887	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815895	0.88[CEU][hapmap]
rs10977149	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12341185	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1998516	0.83[ASW][hapmap]
rs1998517	0.83[ASW][hapmap]
rs2296101	0.89[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2381803	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2381804	0.89[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2381805	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2890796	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs4324967	0.95[CEU][hapmap]
rs6477311	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6477312	0.84[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs7035558	0.89[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs746106	0.92[CEU][hapmap]
rs767674	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767675	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7854860	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

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	chr9:8465600-8482600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:8465800-8484000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:8468600-8484000	Weak transcription	Ovary	ovary
12	chr9:8473200-8483400	Weak transcription	Fetal Stomach	stomach
13	chr9:8473600-8491600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:8474000-8484000	Weak transcription	Brain Angular Gyrus	brain
15	chr9:8474400-8484800	Weak transcription	Fetal Heart	heart
16	chr9:8474400-8485200	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:8475200-8482600	Weak transcription	Dnd41	blood
18	chr9:8475400-8483400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:8475600-8483400	Weak transcription	Brain Substantia Nigra	brain
20	chr9:8476400-8483400	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:8476400-8483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:8476800-8491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:8477000-8482600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:8477000-8491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:8477600-8485000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:8478000-8484000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:8478000-8487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:8478400-8488800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:8478800-8483800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:8478800-8485000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:8478800-8485800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:8479000-8482800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:8479000-8491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:8479200-8483800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:8479400-8485200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:8480400-8483800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:8480400-8484000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:8480600-8483800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:8480600-8484000	Weak transcription	Brain Anterior Caudate	brain
42	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
43	chr9:8481600-8488200	Strong transcription	Fetal Lung	lung
44	chr9:8482200-8482600	Strong transcription	Fetal Brain Male	brain
45	chr9:8482200-8482800	Strong transcription	Fetal Brain Female	brain
46	chr9:8482200-8483000	Strong transcription	Brain Germinal Matrix	brain
47	chr9:8482200-8486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:8482200-8487000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:8482400-8491800	Weak transcription	H9 Cell Line	embryonic stem cell

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