Variant report

Variant	rs10940309
Chromosome Location	chr5:52598099-52598100
allele	A/G
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:10)

rs_ID	r²[population]
rs10491446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10513012	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10805446	1.00[AMR][1000 genomes]
rs10940310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12153223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12153508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12189522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16881115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17341957	1.00[CEU][hapmap]
rs17343328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52585400-52598600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:52596600-52599600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:52596800-52598400	Weak transcription	NHEK	skin
4	chr5:52596800-52599800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:52597000-52600200	Enhancers	NHDF-Ad	bronchial
6	chr5:52597200-52599800	Enhancers	NHLF	lung
7	chr5:52597200-52600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:52597600-52598600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:52597600-52600600	Enhancers	HMEC	breast
10	chr5:52597800-52598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:52597800-52599000	Enhancers	Adipose Nuclei	Adipose
12	chr5:52598000-52599000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:52598000-52599600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:52598000-52599600	Enhancers	Osteobl	bone
15	chr5:52598000-52600600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte 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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