Variant report

Variant	rs6440232
Chromosome Location	chr3:98634012-98634013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57919674..57922229-chr3:98633169..98634718,2	MCF-7	breast:
2	chr3:98631689..98634249-chr3:98634702..98637082,3	MCF-7	breast:
3	chr3:98620790..98623789-chr3:98631975..98634089,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239462	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1036674	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1082401	0.86[AFR][1000 genomes]
rs10935512	1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	1.00[AMR][1000 genomes]
rs1383908	1.00[AMR][1000 genomes]
rs1383911	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1440157	1.00[AMR][1000 genomes]
rs1531736	1.00[AMR][1000 genomes]
rs1600787	0.96[AFR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes]
rs1822019	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1972432	1.00[AMR][1000 genomes]
rs2099738	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2119189	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128053	1.00[AMR][1000 genomes]
rs2173598	1.00[AMR][1000 genomes]
rs2439227	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439230	1.00[AMR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[AMR][1000 genomes]
rs2439235	1.00[AMR][1000 genomes]
rs2448985	1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	1.00[AMR][1000 genomes]
rs2454683	1.00[AMR][1000 genomes]
rs2454690	1.00[AMR][1000 genomes]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	1.00[AMR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	1.00[AMR][1000 genomes]
rs2470858	1.00[AMR][1000 genomes]
rs2470866	1.00[AMR][1000 genomes]
rs2470868	1.00[AMR][1000 genomes]
rs2470874	1.00[AMR][1000 genomes]
rs2470883	1.00[AMR][1000 genomes]
rs278375	1.00[AMR][1000 genomes]
rs278377	1.00[AMR][1000 genomes]
rs278378	1.00[AMR][1000 genomes]
rs278384	1.00[AMR][1000 genomes]
rs278385	1.00[AMR][1000 genomes]
rs278386	1.00[AMR][1000 genomes]
rs278389	1.00[AMR][1000 genomes]
rs2922213	1.00[AMR][1000 genomes]
rs2929488	0.96[AFR][1000 genomes]
rs4273318	1.00[AMR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	1.00[AMR][1000 genomes]
rs7373983	1.00[AMR][1000 genomes]
rs7626395	1.00[AMR][1000 genomes]
rs7630797	1.00[AMR][1000 genomes]
rs774549	0.90[AFR][1000 genomes]
rs828604	1.00[AMR][1000 genomes]
rs828606	1.00[AMR][1000 genomes]
rs828607	1.00[AMR][1000 genomes]
rs828619	1.00[AMR][1000 genomes]
rs828620	1.00[AMR][1000 genomes]
rs828622	1.00[AMR][1000 genomes]
rs828623	1.00[AMR][1000 genomes]
rs828624	1.00[AMR][1000 genomes]
rs866873	1.00[AMR][1000 genomes]
rs965757	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs974981	0.90[AFR][1000 genomes];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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98623600-98636400	Weak transcription	Fetal Heart	heart
2	chr3:98625400-98636600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:98625600-98637200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:98626400-98634400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:98626600-98641600	Weak transcription	NHLF	lung
6	chr3:98632000-98634200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:98632800-98634600	Flanking Active TSS	A549	lung
8	chr3:98632800-98635200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:98633000-98634800	Enhancers	Osteobl	bone
10	chr3:98633200-98635000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:98633400-98634400	Weak transcription	HMEC	breast
12	chr3:98633400-98637200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:98633800-98636400	Weak transcription	NH-A	brain

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