Variant report

Variant	rs7146169
Chromosome Location	chr14:71684656-71684657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCNX-3	chr14:71684523-71684933	ENSG00000258517

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10130213	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158898	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11844320	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850267	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11851589	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109116	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177822	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767266	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990035	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899390	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902916	0.89[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902917	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902918	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55737377	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59985720	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60526802	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60536344	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61174376	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989207	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574006	0.89[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574007	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150921	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153194	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156194	0.93[MEX][hapmap]
rs72726657	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726677	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005089	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs8005615	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005925	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010203	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017895	0.82[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7146169	SLC39A9	cis	parietal	SCAN
rs7146169	PCNX	cis	cerebellum	SCAN
rs7146169	SIPA1L1	cis	cerebellum	SCAN
rs7146169	PCNX	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71679800-71685000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:71680600-71702600	Weak transcription	Brain Angular Gyrus	brain
3	chr14:71680800-71691600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:71680800-71691800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr14:71682400-71687200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:71682600-71694800	Weak transcription	Pancreas	Pancrea
7	chr14:71684600-71685000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr14:71684600-71685000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr14:71684600-71685200	Enhancers	Spleen	Spleen

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