Variant report

Variant	rs2296101
Chromosome Location	chr9:8489006-8489007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10114195	0.91[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10114412	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10117986	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]
rs10119236	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs10125682	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10511497	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10511498	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758976	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10758977	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10815885	0.92[CEU][hapmap];0.84[CHB][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10815886	0.86[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10815887	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10977149	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12341185	0.96[CEU][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1998516	0.94[ASW][hapmap];0.83[YRI][hapmap]
rs1998517	0.94[ASW][hapmap];0.83[YRI][hapmap]
rs2381803	0.87[CEU][hapmap];0.84[CHD][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2381804	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2381805	0.96[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2890796	0.96[CEU][hapmap]
rs4324967	0.91[CEU][hapmap]
rs6477311	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477312	0.89[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs7035558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs746106	0.92[CEU][hapmap]
rs767674	0.96[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs767675	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7854860	0.90[AMR][1000 genomes];0.93[EUR][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	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:8479000-8491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
14	chr9:8482400-8491800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:8483800-8524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:8484400-8492000	Weak transcription	Fetal Stomach	stomach
17	chr9:8484400-8492800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:8484400-8492800	Weak transcription	Brain Substantia Nigra	brain
19	chr9:8486000-8491600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:8486000-8491600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:8486000-8491800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:8486000-8493800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:8486000-8495000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:8486000-8508400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:8486000-8519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:8486000-8522200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:8486200-8491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:8486200-8492000	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:8486200-8492800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:8486200-8501800	Weak transcription	Fetal Heart	heart
31	chr9:8486200-8504600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:8486200-8509000	Weak transcription	Brain Anterior Caudate	brain
33	chr9:8486200-8517200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:8486200-8522800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:8486200-8523200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
37	chr9:8486400-8489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:8486400-8489400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:8486400-8492000	Weak transcription	Fetal Brain Male	brain
40	chr9:8486400-8494000	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:8486400-8494400	Weak transcription	Brain Angular Gyrus	brain
42	chr9:8486400-8494400	Weak transcription	Ovary	ovary
43	chr9:8486600-8507200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:8487000-8499400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:8487000-8521200	Weak transcription	Brain Germinal Matrix	brain
46	chr9:8487000-8521200	Weak transcription	Dnd41	blood
47	chr9:8488000-8492800	Weak transcription	Pancreas	Pancrea
48	chr9:8488200-8489600	Weak transcription	Fetal Lung	lung
49	chr9:8488600-8492000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:8488800-8489600	Weak transcription	Fetal Brain Female	brain

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