Variant report

Variant	rs12003900
Chromosome Location	chr9:18458796-18458797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10511658	1.00[AMR][1000 genomes]
rs11999281	1.00[AMR][1000 genomes]
rs12000949	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12000950	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12001004	1.00[AMR][1000 genomes]
rs12001288	0.87[YRI][hapmap]
rs12001790	0.86[YRI][hapmap]
rs12002126	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12003118	1.00[AMR][1000 genomes]
rs12003267	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs12005242	1.00[AMR][1000 genomes]
rs16936711	1.00[AMR][1000 genomes]
rs16936729	0.83[AFR][1000 genomes]
rs16936775	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs16936777	0.87[YRI][hapmap]
rs16936780	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs16936815	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs1856705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1888064	1.00[AMR][1000 genomes]
rs57153018	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58068158	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58526635	1.00[AMR][1000 genomes]
rs60199560	1.00[AMR][1000 genomes]
rs60288112	1.00[AMR][1000 genomes]
rs60561389	1.00[AMR][1000 genomes]
rs6475217	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7019792	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs7040544	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417101	1.00[AMR][1000 genomes]
rs73418922	1.00[AMR][1000 genomes]
rs73418924	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73418940	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73421011	1.00[AMR][1000 genomes]
rs73421013	1.00[AMR][1000 genomes]
rs73421023	1.00[AMR][1000 genomes]
rs73421030	1.00[AMR][1000 genomes]
rs73421031	1.00[AMR][1000 genomes]
rs73421035	1.00[AMR][1000 genomes]
rs870019	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831522	chr9:18231982-18459492	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18456800-18458800	Enhancers	NHDF-Ad	bronchial
2	chr9:18456800-18459600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:18456800-18459800	Enhancers	HUVEC	blood vessel
4	chr9:18457000-18459800	Enhancers	NHEK	skin
5	chr9:18457200-18459000	Weak transcription	Fetal Intestine Large	intestine
6	chr9:18457200-18461600	Enhancers	HMEC	breast
7	chr9:18457600-18460400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:18457800-18459400	Weak transcription	NH-A	brain
9	chr9:18457800-18463800	Weak transcription	NHLF	lung
10	chr9:18458000-18459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:18458000-18459200	Weak transcription	Osteobl	bone
12	chr9:18458000-18459400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:18458000-18459600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:18458000-18463800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:18458200-18459200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:18458200-18459200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:18458200-18459400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:18458200-18460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:18458600-18458800	Enhancers	Fetal Intestine Small	intestine
20	chr9:18458600-18458800	Enhancers	Hela-S3	cervix
21	chr9:18458600-18459800	Enhancers	HSMMtube	muscle

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