Variant report

Variant	rs1383908
Chromosome Location	chr3:98683663-98683664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98675333..98676915-chr3:98681651..98683756,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs1082398	1.00[EUR][1000 genomes]
rs1082399	1.00[EUR][1000 genomes]
rs1082400	1.00[EUR][1000 genomes]
rs1082402	1.00[EUR][1000 genomes]
rs1082404	1.00[EUR][1000 genomes]
rs1082406	1.00[EUR][1000 genomes]
rs10935512	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1481633	1.00[EUR][1000 genomes]
rs1531736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1600788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1818053	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2133575	0.98[AFR][1000 genomes]
rs2173598	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2439235	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2448985	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes]
rs2454672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2454683	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2454690	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470820	0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470839	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470850	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470856	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470858	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470866	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470868	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470874	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470884	0.98[AFR][1000 genomes]
rs278375	0.84[ASW][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs278377	1.00[AMR][1000 genomes]
rs278378	1.00[AMR][1000 genomes]
rs278384	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs278385	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs278386	1.00[AMR][1000 genomes]
rs278389	1.00[AMR][1000 genomes]
rs2922213	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2929491	0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4857107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5013928	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6440189	0.81[AFR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.95[AFR][1000 genomes]
rs7373983	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73858658	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs774536	1.00[EUR][1000 genomes]
rs774543	1.00[EUR][1000 genomes]
rs774546	1.00[EUR][1000 genomes]
rs774548	1.00[EUR][1000 genomes]
rs828604	0.84[ASW][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs828606	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs828607	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs828611	0.92[YRI][hapmap]
rs828619	1.00[AMR][1000 genomes]
rs828620	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs828622	1.00[AMR][1000 genomes]
rs828623	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs828624	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866873	1.00[AMR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs974982	0.81[AFR][1000 genomes]
rs9883226	1.00[YRI][hapmap]
rs996199	1.00[YRI][hapmap];0.98[AFR][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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98681400-98684200	Enhancers	NHLF	lung
2	chr3:98681400-98684400	Enhancers	NHDF-Ad	bronchial
3	chr3:98681400-98686000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:98681800-98683800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:98681800-98685800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:98682200-98684200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:98682400-98684000	Enhancers	NH-A	brain
8	chr3:98682400-98684200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:98682400-98684200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:98682400-98685200	Weak transcription	HUVEC	blood vessel
11	chr3:98682400-98685800	Enhancers	HMEC	breast
12	chr3:98682400-98686000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:98682600-98684200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:98682800-98683800	Enhancers	Fetal Brain Male	brain
15	chr3:98683000-98685600	Enhancers	NHEK	skin
16	chr3:98683000-98686000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:98683200-98683800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98683200-98683800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:98683200-98684000	Flanking Active TSS	A549	lung
20	chr3:98683200-98684000	Enhancers	HSMM	muscle
21	chr3:98683200-98684200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr3:98683200-98684400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:98683400-98685400	Weak transcription	Osteobl	bone
24	chr3:98683400-98687600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:98683600-98684400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links