Variant report

Variant	rs9302604
Chromosome Location	chr16:69576894-69576895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69576145..69578016-chr16:69598212..69600688,2	MCF-7	breast:
2	chr16:69574674..69576920-chr16:69578465..69580569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11075726	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075729	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11640319	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11641686	0.99[ASN][1000 genomes]
rs11641722	0.99[ASN][1000 genomes]
rs11646575	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11648335	0.91[ASN][1000 genomes]
rs1469908	0.81[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs1972659	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2161630	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917670	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2965749	0.84[JPT][hapmap]
rs3848278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4633710	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57497992	0.98[ASN][1000 genomes]
rs6499231	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499241	0.81[ASN][1000 genomes]
rs7187634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7189878	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7191292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7192380	0.96[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs7192543	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7204433	0.99[ASN][1000 genomes]
rs7205551	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8049728	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8055756	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8061052	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8061725	0.99[ASN][1000 genomes]
rs9783756	0.99[ASN][1000 genomes]
rs9938213	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][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	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv906821	chr16:69509506-69576894	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9302604	LCAT	cis	cerebellum	SCAN
rs9302604	CHST4	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69569800-69579800	Weak transcription	Placenta	Placenta
2	chr16:69570000-69577000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr16:69574200-69577000	Weak transcription	A549	lung
4	chr16:69574600-69577000	Weak transcription	Hela-S3	cervix
5	chr16:69574600-69597800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr16:69576600-69577600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr16:69576800-69577200	Enhancers	NHDF-Ad	bronchial
8	chr16:69576800-69577400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr16:69576800-69577400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr16:69576800-69577400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr16:69576800-69577400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr16:69576800-69577400	Enhancers	Osteobl	bone
13	chr16:69576800-69577600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr16:69576800-69577600	Enhancers	NHLF	lung
15	chr16:69576800-69578000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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