Variant report

Variant	rs2100454
Chromosome Location	chr2:55662423-55662424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC88A-1	chr2:55662292-55662758	NONHSAT070788

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10169185	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10198652	1.00[ASW][hapmap]
rs11125568	0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11125569	0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11125572	0.85[JPT][hapmap]
rs11695152	0.89[ASN][1000 genomes]
rs12618795	0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1598163	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17792710	1.00[ASW][hapmap]
rs1902056	0.81[CHB][hapmap]
rs1902057	0.82[CHB][hapmap]
rs1902061	0.84[JPT][hapmap]
rs2043713	1.00[ASW][hapmap]
rs2045132	0.82[CHB][hapmap]
rs2576688	1.00[ASW][hapmap];0.82[CHB][hapmap]
rs2589057	0.82[CHB][hapmap]
rs2589068	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs2589069	0.82[CHB][hapmap]
rs2589078	0.82[CHB][hapmap]
rs28501559	0.86[ASN][1000 genomes]
rs2867194	0.86[JPT][hapmap]
rs2920963	1.00[YRI][hapmap]
rs3099081	0.81[CHB][hapmap]
rs3099083	0.82[CHB][hapmap]
rs4233961	1.00[ASW][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4352263	0.94[ASN][1000 genomes]
rs4672032	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4672033	0.87[ASN][1000 genomes]
rs4672034	0.86[ASN][1000 genomes]
rs4672035	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4672045	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs56225989	0.89[ASN][1000 genomes]
rs6545489	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6545490	0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6709204	0.87[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs6724840	0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7559987	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7586440	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs7589279	0.82[CHB][hapmap]
rs7595396	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7601340	0.93[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv961778	chr2:55659501-55668562	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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