Variant report

Variant	rs55658250
Chromosome Location	chr3:119597558-119597559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1054190	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11914561	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11915898	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11919783	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11923782	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11923854	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11927667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1381841	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17204605	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17810302	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55644728	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55910624	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56114552	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6765004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68194015	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73175828	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73175830	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73175844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175849	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175858	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175860	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175862	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175864	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175870	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175873	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175877	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175879	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175880	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175886	0.82[AMR][1000 genomes]
rs73175888	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73175891	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73175897	0.95[AFR][1000 genomes]
rs73177904	1.00[AFR][1000 genomes]
rs73177905	0.90[AFR][1000 genomes]
rs73177907	0.90[AFR][1000 genomes]
rs7645180	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
3	chr3:119567000-119605200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
5	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:119577000-119598800	Weak transcription	Fetal Brain Male	brain
7	chr3:119577600-119598200	Weak transcription	Left Ventricle	heart
8	chr3:119577600-119602800	Weak transcription	Psoas Muscle	Psoas
9	chr3:119577600-119607600	Weak transcription	Aorta	Aorta
10	chr3:119577800-119607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:119578000-119601400	Weak transcription	Fetal Intestine Small	intestine
12	chr3:119581800-119605400	Weak transcription	Colonic Mucosa	Colon
13	chr3:119582400-119598400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:119582400-119602200	Weak transcription	A549	lung
15	chr3:119582400-119607400	Weak transcription	Ovary	ovary
16	chr3:119582400-119607600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:119582400-119607600	Weak transcription	Fetal Brain Female	brain
18	chr3:119582400-119607600	Weak transcription	Thymus	Thymus
19	chr3:119582400-119607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:119582400-119610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:119582400-119610600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
26	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
27	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
28	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:119582600-119598400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:119582600-119598400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:119582600-119598800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:119582600-119599000	Weak transcription	NH-A	brain
33	chr3:119582600-119602000	Weak transcription	Hela-S3	cervix
34	chr3:119582600-119602400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:119582600-119602400	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:119582600-119602400	Weak transcription	HSMMtube	muscle
37	chr3:119582600-119602800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:119582600-119607600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:119582600-119607800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:119582600-119609800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:119582600-119610600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:119582600-119611000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:119582600-119611000	Weak transcription	NHLF	lung
44	chr3:119582600-119627200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
46	chr3:119582800-119598400	Weak transcription	Adipose Nuclei	Adipose
47	chr3:119582800-119598400	Weak transcription	Liver	Liver
48	chr3:119582800-119607800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:119582800-119621200	Weak transcription	Fetal Intestine Large	intestine
50	chr3:119583000-119598400	Weak transcription	Primary T cells fromperipheralblood	blood

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