Variant report

Variant	rs889551
Chromosome Location	chr16:31260422-31260423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31204218..31206078-chr16:31258405..31260690,2	K562	blood:
2	chr16:31231842..31234497-chr16:31258086..31260993,2	K562	blood:
3	chr16:31260386..31262455-chr16:31263713..31265453,2	MCF-7	breast:
4	chr16:31252663..31255593-chr16:31260299..31264872,4	MCF-7	breast:
5	chr16:31247262..31249544-chr16:31259534..31262462,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10438639	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1052352	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs11150613	0.86[CHB][hapmap]
rs11150614	0.82[GIH][hapmap]
rs11150616	0.80[GIH][hapmap]
rs11574631	0.86[CHB][hapmap];0.80[GIH][hapmap]
rs11641624	0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11645526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11864632	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs11865830	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449089	0.81[ASN][1000 genomes]
rs12929077	0.92[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs13336592	0.87[CEU][hapmap]
rs17708638	0.82[GIH][hapmap];0.95[MEX][hapmap]
rs1808430	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011491	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2288005	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs2359661	0.80[CEU][hapmap];0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2735393	0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs3087796	0.83[CHB][hapmap]
rs3764327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815801	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077810	0.87[ASW][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs4447446	0.84[ASN][1000 genomes]
rs4459557	0.86[CHB][hapmap]
rs4561481	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597342	0.87[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs4889537	0.92[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs4889538	0.86[AMR][1000 genomes]
rs4889633	0.84[AMR][1000 genomes]
rs4889639	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4889640	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60660286	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6565225	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7186832	0.92[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs7187143	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs7193943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7196256	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206295	0.87[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs741810	0.92[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs7499192	0.87[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8044075	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047985	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048583	0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051304	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056505	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs8057320	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8060268	0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs8062426	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889549	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929868	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9673519	0.88[CHB][hapmap]
rs9923270	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9938177	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv1066073	chr16:31219071-31278572	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs889551	FUS	cis	cerebellum	SCAN
rs889551	MYST1	cis	parietal	SCAN
rs889551	YPEL3	cis	parietal	SCAN
rs889551	ITGAX	cis	lymphoblastoid	seeQTL
rs889551	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx
rs889551	RABEP2	cis	cerebellum	SCAN
rs889551	CD19	cis	cerebellum	SCAN
rs889551	ITGAM	cis	lymphoblastoid	seeQTL
rs889551	TUFM	cis	parietal	SCAN
rs889551	QPRT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31250400-31262600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:31256600-31264000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:31256600-31264200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:31258000-31263400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr16:31259000-31260600	Enhancers	HMEC	breast
6	chr16:31259000-31260800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr16:31259200-31260600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:31259200-31260600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:31259200-31261600	Enhancers	K562	blood
10	chr16:31260400-31260600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr16:31260400-31260600	Enhancers	Lung	lung
12	chr16:31260400-31265000	Weak transcription	NHEK	skin

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