Variant report

Variant	rs17105346
Chromosome Location	chr14:72452471-72452472
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72452453..72454592-chr14:72458480..72460555,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1009017	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11158920	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs11158921	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs11158926	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11158927	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11620690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11622507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11623535	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs11625937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11627768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628133	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11628574	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs12148043	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12433721	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1476745	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs17093750	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs17104493	0.81[EUR][1000 genomes]
rs17105566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17105606	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17105690	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs17768361	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1987722	0.93[ASN][1000 genomes]
rs1987723	0.92[ASN][1000 genomes]
rs2010846	0.93[ASN][1000 genomes]
rs2010850	0.93[ASN][1000 genomes]
rs2052015	0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs2067856	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs2159457	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs2190864	0.88[JPT][hapmap]
rs2238277	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2238280	0.93[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap]
rs2332705	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784058	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4243640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4350510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4354860	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs4899409	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4899412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4902958	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4902966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs56743778	0.84[EUR][1000 genomes]
rs58890880	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59631889	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60503142	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699358	0.93[ASN][1000 genomes]
rs72734102	0.83[EUR][1000 genomes]
rs72735921	0.84[EUR][1000 genomes]
rs72735923	0.84[EUR][1000 genomes]
rs72735952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72735955	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72735956	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728497	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs7493353	0.82[EUR][1000 genomes]
rs7494103	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs8013467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17105346	PCNX	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72446000-72457000	Weak transcription	Right Ventricle	heart
2	chr14:72450200-72453400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr14:72450400-72453000	Weak transcription	Left Ventricle	heart
4	chr14:72450400-72453200	Weak transcription	Right Atrium	heart
5	chr14:72452000-72453200	Flanking Active TSS	Fetal Heart	heart
6	chr14:72452000-72453400	Enhancers	Fetal Stomach	stomach
7	chr14:72452200-72452800	Enhancers	Fetal Lung	lung
8	chr14:72452200-72453000	Enhancers	Colon Smooth Muscle	Colon
9	chr14:72452200-72453000	Enhancers	Rectal Smooth Muscle	rectum
10	chr14:72452200-72453000	Enhancers	Stomach Smooth Muscle	stomach
11	chr14:72452200-72456600	Enhancers	Fetal Brain Male	brain
12	chr14:72452400-72452800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr14:72452400-72452800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:72452400-72452800	Enhancers	Brain Cingulate Gyrus	brain
15	chr14:72452400-72452800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr14:72452400-72453000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr14:72452400-72453000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:72452400-72454400	Enhancers	Fetal Muscle Leg	muscle

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