Variant report

Variant	rs1543973
Chromosome Location	chr2:50569117-50569118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10187911	0.83[JPT][hapmap];0.95[MEX][hapmap]
rs10210298	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11903097	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12053271	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12474009	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13383372	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13404855	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13407780	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1402121	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1520445	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs17040471	0.80[AMR][1000 genomes]
rs17040473	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17040490	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17040542	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17040552	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17040606	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1879320	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1915170	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1915172	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1969351	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1972311	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2139629	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2176853	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2176854	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2176855	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2882692	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4450643	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4493303	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4563262	0.86[MEX][hapmap]
rs4971557	1.00[JPT][hapmap]
rs4971670	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs5019239	1.00[JPT][hapmap]
rs59392224	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6727675	0.81[ASN][1000 genomes]
rs7560420	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7560724	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7575728	1.00[JPT][hapmap]
rs7599052	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1000087	chr2:50501395-50581229	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50548400-50570600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:50560800-50569600	Weak transcription	Fetal Brain Female	brain
3	chr2:50562600-50570800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:50563400-50571200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:50564000-50569400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:50564000-50571000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:50564200-50571400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:50566000-50570000	Weak transcription	Brain Germinal Matrix	brain
9	chr2:50568200-50569600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:50569000-50570800	Enhancers	Fetal Brain Male	brain

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