Variant report

Variant	rs10991679
Chromosome Location	chr9:108276607-108276608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1048215	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10491809	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816281	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10816283	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816285	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816286	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816287	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816288	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10816289	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10820804	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10820811	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820815	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10978169	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10978172	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10978176	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10978177	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10978179	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10991659	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10991673	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10991677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11562356	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12336250	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12336844	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12337780	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12345599	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12352975	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1327352	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1327355	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1887367	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296750	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2417625	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28542455	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28851907	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3750500	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3793639	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3818598	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55798036	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023302	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7023520	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7033138	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7033165	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7034149	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037104	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037141	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7037218	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7038407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047791	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72744263	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72744264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7852541	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7854411	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7856617	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7857186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997319	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
3	chr9:108222200-108277000	Weak transcription	Ovary	ovary
4	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
5	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:108233600-108277000	Weak transcription	Adipose Nuclei	Adipose
8	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
9	chr9:108258200-108277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:108258200-108282000	Weak transcription	Psoas Muscle	Psoas
11	chr9:108258400-108276800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:108258400-108276800	Weak transcription	Brain Germinal Matrix	brain
13	chr9:108259000-108277000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:108259600-108282000	Weak transcription	HSMMtube	muscle
15	chr9:108262800-108277000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:108262800-108277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:108263000-108277400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:108264800-108277000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:108265400-108277000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:108265600-108276800	Weak transcription	Dnd41	blood
21	chr9:108266200-108277400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:108266400-108277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:108266600-108278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:108266600-108278000	Weak transcription	K562	blood
25	chr9:108266600-108282000	Weak transcription	Hela-S3	cervix
26	chr9:108266800-108277000	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:108266800-108277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:108268000-108277200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:108268000-108277200	Weak transcription	Right Ventricle	heart
30	chr9:108268200-108277200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:108268200-108277400	Weak transcription	Fetal Brain Male	brain
32	chr9:108268200-108279000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:108268200-108279600	Weak transcription	Fetal Kidney	kidney
34	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
35	chr9:108269200-108277000	Weak transcription	Fetal Intestine Small	intestine
36	chr9:108269200-108282000	Weak transcription	Pancreas	Pancrea
37	chr9:108269400-108277200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:108269400-108280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:108269600-108276800	Weak transcription	Fetal Brain Female	brain
40	chr9:108269800-108276800	Weak transcription	A549	lung
41	chr9:108269800-108277200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:108269800-108282000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:108269800-108286200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:108270000-108277400	Weak transcription	HepG2	liver
45	chr9:108270800-108277000	Weak transcription	Fetal Stomach	stomach
46	chr9:108270800-108280200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:108271000-108277000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:108271000-108277000	Weak transcription	Fetal Intestine Large	intestine
49	chr9:108271200-108280200	Weak transcription	Colon Smooth Muscle	Colon
50	chr9:108272600-108277200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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