Variant report

Variant	rs56296554
Chromosome Location	chr4:120653942-120653943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11098535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098536	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098537	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005547	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005814	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55922435	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085109	0.91[AMR][1000 genomes]
rs56199127	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56324051	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678594	0.91[AMR][1000 genomes]
rs72678595	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678596	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678597	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678599	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678601	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678602	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680932	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680933	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680934	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680935	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680936	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680937	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680938	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680944	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680945	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680951	0.91[AMR][1000 genomes]
rs72680952	0.82[AMR][1000 genomes]
rs72680953	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680958	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680959	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680964	0.91[AMR][1000 genomes]
rs72680965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680967	0.91[AMR][1000 genomes]
rs72680968	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680969	0.91[AMR][1000 genomes]
rs72680972	0.96[EUR][1000 genomes]
rs72680973	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680974	0.91[AMR][1000 genomes]
rs72680975	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72680976	0.91[AMR][1000 genomes]
rs72680978	0.91[AMR][1000 genomes]
rs72680980	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680982	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680985	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680987	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680989	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680990	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72680995	0.91[AMR][1000 genomes]
rs72681002	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72682804	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72682807	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7659472	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682717	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	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
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1010638	chr4:120586178-120671835	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009771	chr4:120590902-120665812	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1803992	chr4:120649398-120665812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120649600-120658200	Enhancers	NHLF	lung
2	chr4:120650200-120658000	Enhancers	HSMMtube	muscle
3	chr4:120650200-120658400	Enhancers	NHDF-Ad	bronchial
4	chr4:120650400-120657200	Weak transcription	Psoas Muscle	Psoas
5	chr4:120651200-120656000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:120651400-120654000	Enhancers	Placenta	Placenta
7	chr4:120651600-120656000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:120651600-120658000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:120651800-120656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:120651800-120656000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:120652000-120658600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:120652200-120656200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:120652200-120656200	Weak transcription	A549	lung
14	chr4:120652200-120658200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:120652400-120655800	Weak transcription	HMEC	breast
16	chr4:120652600-120654200	Enhancers	Fetal Heart	heart
17	chr4:120652600-120655800	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:120652800-120656000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:120653000-120654400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:120653000-120654600	Weak transcription	NH-A	brain
21	chr4:120653000-120654800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:120653000-120656000	Weak transcription	Hela-S3	cervix
23	chr4:120653200-120654400	Weak transcription	Osteobl	bone
24	chr4:120653200-120654600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:120653200-120655200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:120653200-120655800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:120653200-120657200	Weak transcription	Aorta	Aorta
28	chr4:120653400-120654800	Weak transcription	HSMM	muscle
29	chr4:120653400-120655800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:120653400-120656000	Weak transcription	Fetal Stomach	stomach
31	chr4:120653400-120656000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:120653400-120656200	Weak transcription	Fetal Kidney	kidney
33	chr4:120653600-120655400	Weak transcription	Fetal Lung	lung
34	chr4:120653600-120655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:120653600-120656000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:120653600-120656000	Weak transcription	Stomach Mucosa	stomach

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