Variant report

Variant	rs2336040
Chromosome Location	chr3:21747900-21747901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12638523	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081227	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34736466	0.81[AMR][1000 genomes]
rs62237452	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6764199	0.88[EUR][1000 genomes]
rs6775498	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9310654	0.89[EUR][1000 genomes]
rs9310655	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813051	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9833071	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833350	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862240	0.89[EUR][1000 genomes]
rs9869922	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9871400	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][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	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010460	chr3:21516810-21839871	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834631	chr3:21612283-21763887	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1007048	chr3:21666807-21865229	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv536516	chr3:21666807-21865229	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21732800-21757600	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:21737800-21753600	Weak transcription	Aorta	Aorta
3	chr3:21745000-21748200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:21745600-21748600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:21746200-21748600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:21746400-21748000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:21746400-21748600	Enhancers	HMEC	breast
8	chr3:21746400-21749000	Enhancers	NHDF-Ad	bronchial
9	chr3:21747000-21748000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:21747000-21748000	Enhancers	Hela-S3	cervix
11	chr3:21747000-21748200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:21747000-21748200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:21747000-21748200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:21747200-21748400	Enhancers	NHLF	lung
15	chr3:21747600-21748600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:21747600-21749800	Weak transcription	Psoas Muscle	Psoas
17	chr3:21747800-21748200	Enhancers	Liver	Liver
18	chr3:21747800-21748400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:21747800-21750800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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