Variant report

Variant	rs2519539
Chromosome Location	chr12:119916218-119916219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:119614742..119619324-chr12:119914452..119918204,4	MCF-7	breast:
2	chr12:119913085..119915232-chr12:119915354..119917050,2	MCF-7	breast:
3	chr12:119882836..119888025-chr12:119914651..119920477,9	MCF-7	breast:
4	chr12:119915459..119919519-chr12:119922678..119926603,4	MCF-7	breast:
5	chr12:119894815..119897126-chr12:119915080..119916947,2	MCF-7	breast:
6	chr12:119883274..119886371-chr12:119915842..119918823,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152137	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10774498	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1619163	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1620946	1.00[YRI][hapmap]
rs1622645	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs1716433	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716446	1.00[CEU][hapmap]
rs1727387	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1727390	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2519540	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2519542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695503	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2727742	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6490255	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs697892	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs708874	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708875	1.00[YRI][hapmap]
rs708879	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs784841	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs784844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs784853	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs810784	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047036	chr12:119477583-119992640	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv916688	chr12:119801814-120044407	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832529	chr12:119863378-120071646	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links