Variant report

Variant	rs9823958
Chromosome Location	chr3:139554677-139554678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11717242	1.00[ASN][1000 genomes]
rs11720375	1.00[ASN][1000 genomes]
rs1447721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447723	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1447724	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530648	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562494	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs756252	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs787266	1.00[ASN][1000 genomes]
rs9820731	1.00[CHB][hapmap]
rs9874196	1.00[CHB][hapmap]

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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139549800-139557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:139550000-139554800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:139550600-139554800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:139550600-139555000	Weak transcription	Psoas Muscle	Psoas
5	chr3:139550600-139555600	Weak transcription	Fetal Brain Female	brain
6	chr3:139551200-139555200	Weak transcription	Right Atrium	heart
7	chr3:139552200-139555600	Weak transcription	Fetal Lung	lung
8	chr3:139553200-139558800	Enhancers	Pancreas	Pancrea
9	chr3:139554000-139554800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:139554200-139556400	Enhancers	HSMMtube	muscle
11	chr3:139554400-139557000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:139554600-139554800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:139554600-139555000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:139554600-139555400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:139554600-139556200	Enhancers	Adipose Nuclei	Adipose
16	chr3:139554600-139556800	Enhancers	Ovary	ovary
17	chr3:139554600-139558800	Enhancers	Fetal Brain Male	brain

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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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