Variant report

Variant	rs889515
Chromosome Location	chr16:75251299-75251300
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	chr16:75240295..75242231-chr16:75249759..75251625,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168928	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1019539	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs1035540	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10871304	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs1107593	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11149811	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs11641896	0.90[EUR][1000 genomes]
rs12918452	0.85[EUR][1000 genomes]
rs12924999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1808427	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1862738	0.87[EUR][1000 genomes]
rs2870471	0.80[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2870472	0.93[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3169330	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4479268	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs4737	1.00[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4888361	0.91[EUR][1000 genomes]
rs4888362	0.81[EUR][1000 genomes]
rs4888363	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs4888364	0.90[EUR][1000 genomes]
rs4888365	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6564221	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs6564239	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6564241	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6564243	0.90[EUR][1000 genomes]
rs7195938	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7202566	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7205074	0.82[TSI][hapmap]
rs8048371	0.91[EUR][1000 genomes]
rs8048956	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8059190	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs8061356	0.87[EUR][1000 genomes]
rs889514	0.85[EUR][1000 genomes]
rs9319481	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9927264	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9928842	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs889515	CNTNAP4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75243400-75252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:75244400-75252200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr16:75246800-75261000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:75249400-75254000	Enhancers	Placenta	Placenta
5	chr16:75249600-75251800	Enhancers	Pancreas	Pancrea
6	chr16:75249800-75251400	Bivalent Enhancer	HepG2	liver
7	chr16:75250000-75251800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:75250200-75254000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr16:75251000-75251400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:75251200-75251400	Enhancers	Spleen	Spleen
11	chr16:75251200-75251600	Enhancers	HMEC	breast
12	chr16:75251200-75252200	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links