Variant report

Variant	rs12379687
Chromosome Location	chr9:16854367-16854368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10962638	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962642	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10962645	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962647	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962648	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962649	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10962652	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10962653	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10962656	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10962658	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10962659	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11788047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11789875	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11792249	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17743955	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs62541877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62541878	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62541879	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62541920	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62541922	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62541923	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62541926	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892651	chr9:16816755-16869240	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	esv1814340	chr9:16851678-16865699	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16829800-16864200	Weak transcription	NH-A	brain
2	chr9:16831000-16859600	Weak transcription	HSMM	muscle
3	chr9:16831200-16863400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:16831200-16864400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:16833800-16863800	Weak transcription	NHLF	lung
6	chr9:16836200-16864400	Weak transcription	NHDF-Ad	bronchial
7	chr9:16852800-16857800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:16853000-16854600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:16853000-16864400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:16853200-16863800	Weak transcription	Osteobl	bone
11	chr9:16853400-16854600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:16853400-16856200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:16853400-16860800	Weak transcription	Ovary	ovary
14	chr9:16853400-16863200	Weak transcription	Fetal Stomach	stomach
15	chr9:16853400-16864400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:16854000-16854600	Enhancers	Colon Smooth Muscle	Colon
17	chr9:16854000-16863800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:16854200-16857600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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