Variant report

Variant	rs3109370
Chromosome Location	chr4:120546307-120546308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10013852	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10021469	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13119104	0.82[AFR][1000 genomes]
rs13125819	0.82[AFR][1000 genomes]
rs2389871	0.81[AFR][1000 genomes]
rs2389872	0.83[AMR][1000 genomes]
rs2389876	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2389877	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2389878	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2389884	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2928991	0.82[AFR][1000 genomes]
rs2953290	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2953294	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4146266	0.82[AFR][1000 genomes]
rs4833621	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6534145	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6534148	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6831062	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6854072	0.84[AFR][1000 genomes]
rs7439678	0.82[AFR][1000 genomes]
rs9307480	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:120532400-120547600	Weak transcription	Lung	lung
8	chr4:120533600-120547400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:120534000-120547400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:120537000-120547400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:120541400-120547600	Weak transcription	Left Ventricle	heart
12	chr4:120542600-120547800	Weak transcription	Small Intestine	intestine
13	chr4:120542800-120546600	Weak transcription	Right Atrium	heart
14	chr4:120542800-120547600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:120543200-120547000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:120543200-120547600	Weak transcription	Pancreas	Pancrea
17	chr4:120544400-120550600	Active TSS	Aorta	Aorta
18	chr4:120544600-120547400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:120544600-120547600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:120544600-120547600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:120544800-120546600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:120544800-120546600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:120544800-120547000	Weak transcription	NH-A	brain
24	chr4:120544800-120550800	Active TSS	Stomach Smooth Muscle	stomach
25	chr4:120545000-120549000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr4:120545200-120549000	Active TSS	Duodenum Mucosa	Duodenum
27	chr4:120545200-120550400	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr4:120545200-120550600	Active TSS	Colon Smooth Muscle	Colon
29	chr4:120545400-120547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:120545600-120550600	Active TSS	Fetal Kidney	kidney
31	chr4:120545800-120546600	Transcr. at gene 5' and 3'	NHLF	lung
32	chr4:120545800-120546800	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr4:120545800-120547800	Active TSS	Adipose Nuclei	Adipose
34	chr4:120545800-120550600	Active TSS	Rectal Smooth Muscle	rectum
35	chr4:120546000-120546400	Enhancers	Fetal Stomach	stomach
36	chr4:120546000-120547400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:120546000-120547400	Weak transcription	NHDF-Ad	bronchial
38	chr4:120546000-120547800	Weak transcription	Stomach Mucosa	stomach
39	chr4:120546000-120550600	Active TSS	Fetal Lung	lung
40	chr4:120546200-120546400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:120546200-120546400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr4:120546200-120546400	Active TSS	Osteobl	bone
43	chr4:120546200-120546600	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr4:120546200-120546800	Weak transcription	Fetal Intestine Large	intestine
45	chr4:120546200-120547400	Weak transcription	Ovary	ovary
46	chr4:120546200-120547600	Active TSS	Fetal Intestine Small	intestine
47	chr4:120546200-120550600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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