Variant report

Variant	rs2083008
Chromosome Location	chr3:100609121-100609122
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1017439	0.80[CHB][hapmap]
rs1370160	0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs1370161	0.80[CHB][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs1436941	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1836986	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1836988	0.80[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1987384	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2083009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317331	0.80[CHB][hapmap];0.88[YRI][hapmap]
rs3821725	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs4328836	0.80[CHB][hapmap]
rs4928058	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4928093	0.86[CHB][hapmap]
rs4928094	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441555	0.84[AFR][1000 genomes]
rs6786325	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs6786332	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs975536	0.83[YRI][hapmap];0.82[AFR][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	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr3:100594400-100618200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:100594600-100616800	Weak transcription	Ovary	ovary
3	chr3:100598600-100612400	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:100599600-100610400	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:100599800-100610600	Weak transcription	Fetal Stomach	stomach
7	chr3:100599800-100618200	Weak transcription	Fetal Lung	lung
8	chr3:100600000-100610400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:100600200-100610200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:100600200-100610400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:100602000-100609200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:100602200-100610200	Weak transcription	Osteobl	bone
13	chr3:100602200-100616800	Weak transcription	NHDF-Ad	bronchial
14	chr3:100604200-100612200	Weak transcription	Psoas Muscle	Psoas
15	chr3:100604200-100617000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:100604400-100611200	Weak transcription	HSMMtube	muscle
17	chr3:100604600-100609600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:100606600-100612000	Enhancers	Hela-S3	cervix
19	chr3:100608000-100609600	Weak transcription	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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