Variant report

Variant	rs62339004
Chromosome Location	chr4:53968372-53968373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12186215	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17702812	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2053650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864446	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62324997	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62338965	0.81[EUR][1000 genomes]
rs62338967	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62338969	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62338970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62338994	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62339002	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53964600-53968400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:53964600-53968400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:53964600-53968400	Enhancers	NHEK	skin
4	chr4:53965800-53971000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:53965800-53971200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:53965800-53971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:53965800-53986000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:53966000-53975000	Weak transcription	Fetal Stomach	stomach
9	chr4:53966800-53968400	Enhancers	HMEC	breast
10	chr4:53967000-53968400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:53967000-53968400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:53967200-53968600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:53967400-53970200	Weak transcription	Fetal Lung	lung
14	chr4:53967400-53971000	Weak transcription	Ovary	ovary
15	chr4:53967600-53969200	Enhancers	HSMM	muscle
16	chr4:53967600-53969600	Enhancers	NHDF-Ad	bronchial
17	chr4:53967600-53970800	Enhancers	HUVEC	blood vessel
18	chr4:53967800-53968400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr4:53967800-53970600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:53968000-53968400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:53968000-53968400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:53968000-53968400	Enhancers	NHLF	lung
23	chr4:53968000-53968600	Enhancers	NH-A	brain
24	chr4:53968000-53969400	Enhancers	Osteobl	bone
25	chr4:53968000-53975200	Weak transcription	Fetal Heart	heart
26	chr4:53968200-53968400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:53968200-53968400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:53968200-53968400	Enhancers	HSMMtube	muscle
29	chr4:53968200-53969600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:53968200-53979200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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