Variant report

Variant	rs2449044
Chromosome Location	chr3:98695282-98695283
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:98695204-98695521	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
LINC00973	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2470789	0.92[ASN][1000 genomes]
rs2929492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56694316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56857413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56914517	1.00[AMR][1000 genomes]
rs57962467	0.97[AFR][1000 genomes]
rs60878971	1.00[AMR][1000 genomes]
rs61228839	1.00[AMR][1000 genomes]
rs72923090	1.00[AMR][1000 genomes]
rs72936606	1.00[AMR][1000 genomes]
rs72938508	1.00[AMR][1000 genomes]
rs72938510	1.00[AMR][1000 genomes]
rs72938540	0.86[AFR][1000 genomes]
rs72938569	1.00[AMR][1000 genomes]
rs72938577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940503	1.00[AMR][1000 genomes]

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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98691000-98696200	Weak transcription	Hela-S3	cervix
2	chr3:98691400-98696400	Weak transcription	HSMM	muscle
3	chr3:98691600-98696400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:98691800-98696000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:98691800-98696400	Weak transcription	NHLF	lung
6	chr3:98692000-98695400	Weak transcription	Osteobl	bone
7	chr3:98692000-98696000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:98692000-98696000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:98692000-98696200	Weak transcription	NHEK	skin
10	chr3:98692000-98696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:98692000-98699600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:98693600-98696400	Weak transcription	NHDF-Ad	bronchial
13	chr3:98693600-98697400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:98694600-98695400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:98695000-98695600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:98695000-98696400	Enhancers	A549	lung
17	chr3:98695000-98696400	Enhancers	HUVEC	blood vessel
18	chr3:98695000-98697800	Enhancers	HMEC	breast
19	chr3:98695200-98695400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:98695200-98695600	Enhancers	NH-A	brain
21	chr3:98695200-98696400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:98695200-98696400	Enhancers	Muscle Satellite Cultured Cells	--

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