Variant report

Variant	rs595993
Chromosome Location	chr3:54660276-54660277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1366032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483200	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs495532	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs496625	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs499292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500382	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs508907	0.88[CEU][hapmap]
rs551799	0.89[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs573279	0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs595040	0.99[EUR][1000 genomes]
rs605284	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs616113	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs626074	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs661201	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs667612	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs670335	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs674542	0.95[EUR][1000 genomes];0.89[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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv979836	chr3:54659941-54661074	Weak transcription Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54654800-54662400	Weak transcription	Right Atrium	heart
5	chr3:54655000-54662400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:54655600-54662800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:54658800-54662800	Weak transcription	Ovary	ovary
8	chr3:54659200-54664600	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:54659800-54660400	Enhancers	Esophagus	oesophagus
10	chr3:54659800-54662800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:54659800-54664400	Weak transcription	Spleen	Spleen

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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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