Variant report

Variant	rs58671569
Chromosome Location	chr3:138394873-138394874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12107289	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12108068	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28473201	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3729699	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57216562	1.00[AMR][1000 genomes]
rs59797415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59813438	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60295689	1.00[AMR][1000 genomes]
rs60850836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6795773	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982685	0.88[AFR][1000 genomes]
rs72988872	0.91[AFR][1000 genomes]
rs72988878	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990507	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990541	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990552	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990569	1.00[AMR][1000 genomes]
rs72990577	1.00[AMR][1000 genomes]
rs73866224	1.00[AMR][1000 genomes]
rs7635120	1.00[AFR][1000 genomes]
rs7648802	0.90[AFR][1000 genomes]
rs7649131	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
2	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
3	chr3:138368800-138400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:138368800-138422600	Weak transcription	Right Atrium	heart
5	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
6	chr3:138369200-138401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:138369200-138412800	Weak transcription	Hela-S3	cervix
8	chr3:138369200-138428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:138369200-138435600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:138374800-138397000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:138375200-138429000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:138383000-138395000	Weak transcription	Fetal Brain Female	brain
13	chr3:138383000-138404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:138383200-138395400	Weak transcription	Colonic Mucosa	Colon
15	chr3:138383200-138412800	Weak transcription	Ovary	ovary
16	chr3:138383200-138448200	Weak transcription	Gastric	stomach
17	chr3:138383400-138395000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:138383400-138395400	Weak transcription	HSMMtube	muscle
19	chr3:138383400-138426400	Weak transcription	Spleen	Spleen
20	chr3:138383400-138443000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:138383800-138400200	Weak transcription	Fetal Kidney	kidney
22	chr3:138383800-138405400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:138384000-138395000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:138384000-138395800	Weak transcription	Fetal Stomach	stomach
25	chr3:138385000-138396200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:138385000-138418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:138388400-138399600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:138388600-138395200	Weak transcription	Placenta	Placenta
29	chr3:138389200-138401200	Weak transcription	Brain Substantia Nigra	brain
30	chr3:138389200-138405000	Weak transcription	Small Intestine	intestine
31	chr3:138390800-138459600	Weak transcription	Right Ventricle	heart
32	chr3:138391200-138422000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:138391800-138395000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:138392200-138395800	ZNF genes & repeats	GM12878-XiMat	blood
35	chr3:138392200-138405600	Weak transcription	Stomach Mucosa	stomach
36	chr3:138392400-138396200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:138392400-138396400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:138392400-138396400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:138392600-138395800	Strong transcription	Liver	Liver
40	chr3:138392600-138397400	Strong transcription	Fetal Thymus	thymus
41	chr3:138392800-138395200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:138392800-138395800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:138393000-138395000	Weak transcription	NH-A	brain
44	chr3:138393000-138395800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr3:138393000-138395800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr3:138393000-138396000	ZNF genes & repeats	Dnd41	blood
47	chr3:138393200-138395000	Weak transcription	NHDF-Ad	bronchial
48	chr3:138393200-138395200	Weak transcription	Adipose Nuclei	Adipose
49	chr3:138393200-138395200	Weak transcription	Fetal Heart	heart
50	chr3:138393200-138395800	Weak transcription	Lung	lung

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