Variant report

Variant	rs1518399
Chromosome Location	chr2:58231314-58231315
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	chr2:58230955..58233450-chr2:58273896..58276071,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10172212	0.83[JPT][hapmap]
rs10188070	0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs1040224	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1040225	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12620940	0.83[AMR][1000 genomes]
rs12622856	0.84[JPT][hapmap]
rs12713370	0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1401100	1.00[JPT][hapmap]
rs1518395	0.81[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568252	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568253	1.00[JPT][hapmap]
rs2043890	0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs2139053	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2312147	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465804	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678870	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678880	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2678889	1.00[JPT][hapmap]
rs2678897	1.00[JPT][hapmap]
rs2678901	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678903	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678905	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678906	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678908	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2678910	0.81[AFR][1000 genomes]
rs2717001	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2717002	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2717004	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2717006	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2717019	1.00[JPT][hapmap]
rs2717023	1.00[JPT][hapmap]
rs2717024	1.00[JPT][hapmap]
rs2717027	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2717031	1.00[JPT][hapmap]
rs2717036	1.00[JPT][hapmap]
rs2717040	1.00[JPT][hapmap]
rs2717043	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs28718871	0.81[AMR][1000 genomes]
rs6545677	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6732310	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs848287	0.83[JPT][hapmap]
rs932188	0.82[ASN][1000 genomes]
rs961522	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs966721	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs968653	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs970941	0.83[CHB][hapmap];1.00[JPT][hapmap]

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	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv458041	chr2:58196110-58237724	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv582096	chr2:58196110-58237724	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No data

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