Variant report

Variant	rs9994643
Chromosome Location	chr4:53551712-53551713
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53524851..53526352-chr4:53551411..53553400,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248866	Chromatin interaction
ENSG00000109189	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10000311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10001370	0.87[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10003396	0.87[ASN][1000 genomes]
rs10010306	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10012676	0.87[ASN][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10020568	0.90[ASN][1000 genomes]
rs10021143	0.93[ASN][1000 genomes]
rs10023867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10027906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10028085	0.90[ASN][1000 genomes]
rs10028755	0.90[ASN][1000 genomes]
rs10029145	0.93[ASN][1000 genomes]
rs10031386	1.00[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10033218	1.00[ASN][1000 genomes]
rs10471216	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13434726	0.87[ASN][1000 genomes]
rs13435157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28376189	0.90[ASN][1000 genomes]
rs28379922	0.90[ASN][1000 genomes]
rs28380682	0.93[ASN][1000 genomes]
rs28402205	1.00[ASN][1000 genomes]
rs28411005	1.00[ASN][1000 genomes]
rs28412170	0.93[ASN][1000 genomes]
rs28430452	1.00[ASN][1000 genomes]
rs28451750	0.93[ASN][1000 genomes]
rs28475600	0.93[ASN][1000 genomes]
rs28482298	0.93[ASN][1000 genomes]
rs28503210	0.93[ASN][1000 genomes]
rs28565016	0.93[ASN][1000 genomes]
rs28588481	0.94[ASN][1000 genomes]
rs28590396	1.00[ASN][1000 genomes]
rs28619184	0.93[ASN][1000 genomes]
rs28644292	0.93[ASN][1000 genomes]
rs28654693	1.00[ASN][1000 genomes]
rs28660550	1.00[ASN][1000 genomes]
rs28660571	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28672279	0.93[ASN][1000 genomes]
rs28694544	0.90[ASN][1000 genomes]
rs28721897	1.00[ASN][1000 genomes]
rs28722174	0.93[ASN][1000 genomes]
rs28784684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28825181	0.90[ASN][1000 genomes]
rs28825412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28849759	1.00[ASN][1000 genomes]
rs28852068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6830833	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7673679	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9990686	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9997863	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53550400-53551800	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr4:53551000-53551800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:53551000-53552000	Flanking Active TSS	GM12878-XiMat	blood
4	chr4:53551200-53551800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:53551400-53553800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:53551600-53551800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links