Variant report

Variant	rs55798036
Chromosome Location	chr9:108279545-108279546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1048215	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10491809	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816281	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816283	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10816285	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816286	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10816287	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816288	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816289	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820804	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978169	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10978172	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10978176	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978177	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10978179	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10991659	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10991673	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11562356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12336250	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12336844	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12337780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12345599	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12352975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327352	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1327355	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1887367	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297023	0.82[ASN][1000 genomes]
rs2417625	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28542455	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28851907	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750500	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793639	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3818598	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7023302	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7033138	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7033165	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7034149	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7037104	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7037141	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7037218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7038407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7047791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72744263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852541	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7854411	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7856617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997319	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[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	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
5	chr9:108258200-108282000	Weak transcription	Psoas Muscle	Psoas
6	chr9:108259600-108282000	Weak transcription	HSMMtube	muscle
7	chr9:108266600-108282000	Weak transcription	Hela-S3	cervix
8	chr9:108268200-108279600	Weak transcription	Fetal Kidney	kidney
9	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
10	chr9:108269200-108282000	Weak transcription	Pancreas	Pancrea
11	chr9:108269400-108280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:108269800-108282000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:108269800-108286200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:108270800-108280200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:108271200-108280200	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:108272600-108282000	Weak transcription	Gastric	stomach
17	chr9:108272800-108282400	Weak transcription	NHLF	lung
18	chr9:108272800-108304600	Weak transcription	NHEK	skin
19	chr9:108273000-108282000	Weak transcription	HSMM	muscle
20	chr9:108273000-108282000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:108273000-108282200	Weak transcription	NH-A	brain
22	chr9:108273000-108282200	Weak transcription	NHDF-Ad	bronchial
23	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
24	chr9:108275200-108282000	Weak transcription	Esophagus	oesophagus
25	chr9:108276000-108282000	Weak transcription	Osteobl	bone
26	chr9:108276200-108309200	Weak transcription	Lung	lung
27	chr9:108276400-108282000	Weak transcription	Spleen	Spleen
28	chr9:108276600-108279600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:108277000-108279600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:108277000-108279600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:108277000-108280200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:108277000-108280200	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:108277200-108279600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:108277600-108282000	Weak transcription	Dnd41	blood
35	chr9:108277600-108282200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:108278000-108281200	Weak transcription	Aorta	Aorta
37	chr9:108278000-108282000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:108278000-108282000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:108278000-108282000	Weak transcription	Left Ventricle	heart
40	chr9:108278000-108282000	Weak transcription	HepG2	liver
41	chr9:108278000-108282600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:108278000-108292800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:108278200-108279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:108278200-108284000	Weak transcription	Adipose Nuclei	Adipose
45	chr9:108278400-108279600	Strong transcription	Fetal Intestine Large	intestine
46	chr9:108278400-108282000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr9:108278400-108282000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:108278600-108279600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:108278600-108282000	Weak transcription	HMEC	breast
50	chr9:108278800-108282000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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