Variant report

Variant	rs56309321
Chromosome Location	chr13:67660087-67660088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:67659257..67661234-chr13:67663464..67666434,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10492596	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10492597	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11148737	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11148738	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12184632	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12184736	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12372837	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408171	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149448	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17195259	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17195266	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17587572	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17791056	0.97[EUR][1000 genomes]
rs260131	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs260140	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs260160	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260162	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260164	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs260165	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56226179	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56915128	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61191692	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959247	0.97[EUR][1000 genomes]
rs61959248	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959249	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959360	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61959362	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959363	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959367	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959407	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61961771	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61961774	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9317637	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9529163	0.84[EUR][1000 genomes]
rs9529166	0.94[EUR][1000 genomes]
rs9529167	0.94[EUR][1000 genomes]
rs9529169	0.94[EUR][1000 genomes]
rs9529174	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9529180	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9529182	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529183	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529185	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9529186	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9529187	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9529188	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9540964	0.84[EUR][1000 genomes]
rs9540967	0.84[EUR][1000 genomes]
rs9540968	0.93[EUR][1000 genomes]
rs9540969	0.94[EUR][1000 genomes]
rs9540971	0.94[EUR][1000 genomes]
rs9540980	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9540982	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540983	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540984	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540987	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540988	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540989	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9540993	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540995	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540996	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540997	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9540998	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9540999	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9541000	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9541001	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9541002	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9541003	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9541004	0.93[EUR][1000 genomes]
rs9541006	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9541007	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9541008	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9645951	0.84[EUR][1000 genomes]
rs972419	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530605	chr13:67126136-67697306	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv900414	chr13:67515590-67701341	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1045093	chr13:67517932-67693875	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv541821	chr13:67517932-67693875	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv430581	chr13:67572850-67762288	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv430582	chr13:67589898-67762299	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1037217	chr13:67589937-67728156	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1039600	chr13:67593961-67726047	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv541823	chr13:67593961-67726047	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56309321	PCDH9	cis	Nerve Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67654200-67660400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:67658600-67661800	Weak transcription	Colon Smooth Muscle	Colon
3	chr13:67658800-67660200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:67658800-67660400	Weak transcription	Brain Angular Gyrus	brain
5	chr13:67658800-67661600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:67658800-67661800	Weak transcription	Adipose Nuclei	Adipose
7	chr13:67658800-67662000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:67658800-67662800	Weak transcription	Brain Substantia Nigra	brain
9	chr13:67659600-67660600	Enhancers	A549	lung
10	chr13:67659600-67661800	Enhancers	Brain Cingulate Gyrus	brain
11	chr13:67659600-67662400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr13:67659800-67661000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:67659800-67661400	Enhancers	Brain Hippocampus Middle	brain
14	chr13:67659800-67661800	Enhancers	Brain Anterior Caudate	brain
15	chr13:67659800-67662400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:67660000-67660800	Enhancers	Liver	Liver
17	chr13:67660000-67661000	Enhancers	Fetal Heart	heart

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