Variant report

Variant	rs2200473
Chromosome Location	chr3:105225340-105225341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11710166	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710857	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11713535	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714275	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714277	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11715283	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716035	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718405	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718457	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719817	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1898655	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1955135	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2399049	0.94[ASN][1000 genomes]
rs2895300	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34029528	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772542	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772544	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772547	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481177	0.94[ASN][1000 genomes]
rs526297	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57986655	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59322590	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs598425	0.94[ASN][1000 genomes]
rs61522255	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6771935	0.85[ASN][1000 genomes]
rs6771987	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786815	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6794273	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73175407	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175433	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175435	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175442	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175449	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175451	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175463	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73175491	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73177465	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73177470	0.85[ASN][1000 genomes]
rs73177478	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73177489	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73177494	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73179378	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73179384	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181374	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181376	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181380	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181387	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181395	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181396	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181397	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73181401	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73183103	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73183108	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183112	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183114	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183115	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183185	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183186	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183187	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183188	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73183198	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73185106	0.87[EUR][1000 genomes]
rs73185114	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73185115	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73189021	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73189028	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189034	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189060	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192730	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192733	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192737	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192751	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73192754	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73192770	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210200-105229000	Weak transcription	HSMM	muscle
2	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:105221600-105229800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:105221600-105231800	Weak transcription	NHLF	lung
6	chr3:105221800-105227600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
8	chr3:105222400-105226800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:105222600-105225600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:105222600-105229000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:105222600-105230000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:105222800-105230400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:105222800-105231800	Weak transcription	NH-A	brain
14	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:105223000-105230000	Weak transcription	A549	lung
16	chr3:105223800-105229000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:105224000-105225400	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:105224000-105225800	Enhancers	Liver	Liver
20	chr3:105224000-105227200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:105224000-105229200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:105224200-105226400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:105224200-105226400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:105224400-105229000	Weak transcription	Gastric	stomach
25	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
26	chr3:105225000-105225800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr3:105225000-105226200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:105225200-105226800	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:105225200-105227000	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links