Variant report

Variant	rs9540999
Chromosome Location	chr13:67679491-67679492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10492596	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10492597	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11148737	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11148738	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12184632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184736	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]
rs12372837	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1408171	0.90[EUR][1000 genomes]
rs149448	0.90[EUR][1000 genomes]
rs17195259	0.90[EUR][1000 genomes]
rs17195266	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17517438	0.82[CEU][hapmap]
rs17587572	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17589427	0.82[CEU][hapmap]
rs17791056	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs260131	0.90[EUR][1000 genomes]
rs260140	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs260160	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs260162	0.90[EUR][1000 genomes]
rs260164	0.90[EUR][1000 genomes]
rs260165	0.90[EUR][1000 genomes]
rs56226179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56309321	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56915128	0.90[EUR][1000 genomes]
rs61191692	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959247	0.90[EUR][1000 genomes]
rs61959248	0.90[EUR][1000 genomes]
rs61959249	0.90[EUR][1000 genomes]
rs61959360	0.81[EUR][1000 genomes]
rs61959362	0.90[EUR][1000 genomes]
rs61959363	0.90[EUR][1000 genomes]
rs61959367	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61959407	0.84[EUR][1000 genomes]
rs61961771	0.88[EUR][1000 genomes]
rs61961774	0.90[EUR][1000 genomes]
rs7987441	0.86[JPT][hapmap]
rs9317637	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9529163	0.85[CEU][hapmap]
rs9529166	0.88[EUR][1000 genomes]
rs9529167	0.88[EUR][1000 genomes]
rs9529169	0.88[EUR][1000 genomes]
rs9529174	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9529180	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9529182	0.90[EUR][1000 genomes]
rs9529183	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9529185	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9529186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529188	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9540967	0.87[CEU][hapmap]
rs9540968	0.86[EUR][1000 genomes]
rs9540969	0.88[EUR][1000 genomes]
rs9540971	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9540980	0.90[EUR][1000 genomes]
rs9540982	0.90[EUR][1000 genomes]
rs9540983	0.90[EUR][1000 genomes]
rs9540984	0.90[EUR][1000 genomes]
rs9540987	0.90[EUR][1000 genomes]
rs9540988	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9540989	0.90[EUR][1000 genomes]
rs9540993	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9540994	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9540995	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9540996	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9540997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9541000	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]
rs9541001	0.81[EUR][1000 genomes]
rs9541002	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]
rs9541003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9541004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9541006	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9541007	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9541008	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9541013	0.82[CEU][hapmap]
rs972419	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv1040715	chr13:67668189-67699198	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv832641	chr13:67671691-67708713	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9540999	PCDH9	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67677000-67680600	Weak transcription	Brain Hippocampus Middle	brain
2	chr13:67678200-67681600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:67678600-67680400	Weak transcription	A549	lung

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