Variant report

Variant	rs10889938
Chromosome Location	chr1:72452050-72452051
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1016126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493489	0.82[CEU][hapmap]
rs10889934	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889936	0.84[ASN][1000 genomes]
rs12024769	0.81[CEU][hapmap]
rs12026691	0.82[CEU][hapmap]
rs12090492	0.83[ASN][1000 genomes]
rs1426173	0.95[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1486089	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1486099	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1486100	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1486102	0.83[ASN][1000 genomes]
rs1486113	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812738	0.84[ASN][1000 genomes]
rs1843582	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1937185	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1937189	0.84[ASN][1000 genomes]
rs2052722	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2114214	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2256783	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2422058	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2422059	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2489821	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2554417	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2630389	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2630411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2630417	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2630418	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2768376	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2768378	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2768395	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2801322	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2801328	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3102902	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102905	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102908	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102911	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102912	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3102917	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102918	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3102923	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102926	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3128550	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3128557	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4111091	0.84[ASN][1000 genomes]
rs6424453	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6424454	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6666863	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7511981	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7544722	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7544750	0.84[ASN][1000 genomes]
rs7550950	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv999162	chr1:72319163-72477496	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv534995	chr1:72319163-72477496	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv428763	chr1:72353556-72499701	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1354	chr1:72431164-72475522	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv546478	chr1:72442018-72512391	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72451600-72452400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:72451800-72452200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:72451800-72452200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:72451800-72452400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:72451800-72452800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:72451800-72453200	Enhancers	Colon Smooth Muscle	Colon
7	chr1:72452000-72452400	Enhancers	Ovary	ovary
8	chr1:72452000-72452400	Enhancers	NH-A	brain
9	chr1:72452000-72453400	Enhancers	Fetal Muscle Leg	muscle
10	chr1:72452000-72453600	Enhancers	Fetal Heart	heart
11	chr1:72452000-72454000	Enhancers	Fetal Stomach	stomach

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