Variant report

Variant	rs11620632
Chromosome Location	chr14:71729438-71729439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11626886	0.85[EUR][1000 genomes]
rs11626990	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11627918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11845249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11849508	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878989	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs12884929	0.80[ASN][1000 genomes]
rs12891975	0.80[ASN][1000 genomes]
rs17767362	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17767380	0.82[EUR][1000 genomes]
rs17767386	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17767398	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17767553	0.81[CHD][hapmap]
rs2108706	0.86[CHB][hapmap]
rs2108708	0.85[EUR][1000 genomes]
rs2159145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34061264	0.80[ASN][1000 genomes]
rs34281405	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34674149	0.81[CHD][hapmap]
rs34911660	0.84[ASN][1000 genomes]
rs4453405	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4899394	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55863348	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56201715	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59697713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989244	0.82[EUR][1000 genomes]
rs61989245	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989246	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989247	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989250	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989252	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61989255	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61989256	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61989257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989259	0.85[EUR][1000 genomes]
rs61991192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61991193	0.82[EUR][1000 genomes]
rs61991195	0.82[EUR][1000 genomes]
rs61991200	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61991213	0.80[ASN][1000 genomes]
rs7142214	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7152842	1.00[CHB][hapmap]
rs7155259	0.83[CEU][hapmap]
rs7156194	0.86[CEU][hapmap]
rs7160460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723966	0.81[CHD][hapmap]
rs72726701	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72728403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72728406	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11620632	PCNX	cis	cerebellum	SCAN
rs11620632	SLC8A3	cis	cerebellum	SCAN
rs11620632	SIPA1L1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71728200-71729600	Enhancers	Osteobl	bone
2	chr14:71729000-71729600	Enhancers	Fetal Heart	heart
3	chr14:71729400-71733600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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