Variant report

Variant	rs2890796
Chromosome Location	chr9:8478511-8478512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10114195	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10114412	0.85[ASN][1000 genomes]
rs10117986	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10119236	0.84[CEU][hapmap]
rs10125682	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10511497	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10511498	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10758976	1.00[CEU][hapmap]
rs10758977	0.96[CEU][hapmap]
rs10815885	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815886	0.94[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10815887	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10815895	0.85[CEU][hapmap]
rs10977149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12341185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296101	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2381803	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2381804	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2381805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4324967	0.92[CEU][hapmap]
rs6477311	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6477312	0.88[CEU][hapmap]
rs7035558	0.96[CEU][hapmap]
rs746106	0.96[CEU][hapmap]
rs767674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7854860	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	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	esv2383382	chr9:8478510-8478511	Strong transcription Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:45 , 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	chr9:8471000-8479200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:8473200-8483400	Weak transcription	Fetal Stomach	stomach
14	chr9:8473600-8491600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:8474000-8484000	Weak transcription	Brain Angular Gyrus	brain
16	chr9:8474200-8480000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:8474400-8484800	Weak transcription	Fetal Heart	heart
18	chr9:8474400-8485200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:8475200-8478800	Weak transcription	Brain Anterior Caudate	brain
20	chr9:8475200-8482600	Weak transcription	Dnd41	blood
21	chr9:8475400-8483400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:8475600-8483400	Weak transcription	Brain Substantia Nigra	brain
23	chr9:8476400-8482200	Weak transcription	Brain Germinal Matrix	brain
24	chr9:8476400-8483400	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:8476400-8483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:8476600-8482200	Weak transcription	Fetal Brain Male	brain
27	chr9:8476800-8491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:8477000-8479000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:8477000-8482600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:8477000-8491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:8477200-8482200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:8477400-8479000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr9:8477600-8479200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr9:8477600-8479400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr9:8477600-8485000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr9:8477800-8478800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr9:8478000-8479200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr9:8478000-8484000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr9:8478000-8487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:8478200-8479000	Strong transcription	Fetal Brain Female	brain
41	chr9:8478200-8480200	Weak transcription	Fetal Lung	lung
42	chr9:8478200-8482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:8478400-8478800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr9:8478400-8488800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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