Variant report

Variant	rs9529163
Chromosome Location	chr13:67575566-67575567
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1022866	1.00[JPT][hapmap]
rs10492596	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10492597	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11148737	0.87[EUR][1000 genomes]
rs11148738	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12184736	0.85[CEU][hapmap]
rs12372837	0.84[EUR][1000 genomes]
rs1323911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1323917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1323923	1.00[JPT][hapmap]
rs1408170	1.00[JPT][hapmap]
rs1408171	0.87[EUR][1000 genomes]
rs149448	0.87[EUR][1000 genomes]
rs17195259	0.87[EUR][1000 genomes]
rs17195266	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17587572	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17791001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17791056	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1924309	1.00[JPT][hapmap]
rs1924310	1.00[JPT][hapmap]
rs260131	0.87[EUR][1000 genomes]
rs260139	1.00[JPT][hapmap]
rs260140	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs260160	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs260162	0.87[EUR][1000 genomes]
rs260164	0.87[EUR][1000 genomes]
rs260165	0.87[EUR][1000 genomes]
rs260168	1.00[JPT][hapmap]
rs56309321	0.84[EUR][1000 genomes]
rs56915128	0.87[EUR][1000 genomes]
rs61191692	0.84[EUR][1000 genomes]
rs61959247	0.87[EUR][1000 genomes]
rs61959248	0.87[EUR][1000 genomes]
rs61959249	0.87[EUR][1000 genomes]
rs61959362	0.87[EUR][1000 genomes]
rs61959363	0.87[EUR][1000 genomes]
rs61959367	0.84[EUR][1000 genomes]
rs61961771	0.84[EUR][1000 genomes]
rs61961774	0.87[EUR][1000 genomes]
rs7981987	1.00[JPT][hapmap]
rs7987190	1.00[JPT][hapmap]
rs7987478	1.00[JPT][hapmap]
rs9317632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9317633	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9317637	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9529158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9529166	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9529167	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9529169	0.89[EUR][1000 genomes]
rs9529170	1.00[JPT][hapmap]
rs9529174	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9529180	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9529181	1.00[JPT][hapmap]
rs9529182	0.87[EUR][1000 genomes]
rs9529183	0.83[EUR][1000 genomes]
rs9529185	0.85[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9529186	0.85[CEU][hapmap]
rs9529187	0.85[CEU][hapmap]
rs9529188	0.85[CEU][hapmap]
rs9540949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9540950	1.00[CHB][hapmap]
rs9540952	1.00[JPT][hapmap]
rs9540953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9540954	1.00[JPT][hapmap]
rs9540956	0.84[ASN][1000 genomes]
rs9540958	0.84[ASN][1000 genomes]
rs9540959	0.84[ASN][1000 genomes]
rs9540960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9540964	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9540967	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9540968	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9540969	0.89[EUR][1000 genomes]
rs9540971	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9540980	1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs9540982	0.87[EUR][1000 genomes]
rs9540983	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9540984	0.87[EUR][1000 genomes]
rs9540987	0.87[EUR][1000 genomes]
rs9540988	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9540989	0.87[EUR][1000 genomes]
rs9540993	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9540994	0.84[EUR][1000 genomes]
rs9540995	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs9540996	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9540999	0.85[CEU][hapmap]
rs9541004	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs9541006	0.85[CEU][hapmap]
rs9541007	0.85[CEU][hapmap]
rs9541008	0.85[CEU][hapmap]
rs9571705	1.00[JPT][hapmap]
rs9645951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs972419	0.83[EUR][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	nsv900407	chr13:67434161-67603745	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv832640	chr13:67460304-67635966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv428604	chr13:67480426-67645030	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv541822	chr13:67550756-67594021	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9529163	PCDH9	cis	Nerve Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67569800-67575600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr13:67569800-67575800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:67569800-67588200	Weak transcription	Brain Angular Gyrus	brain
4	chr13:67571600-67575600	Weak transcription	Brain Substantia Nigra	brain
5	chr13:67571600-67575600	Weak transcription	Gastric	stomach
6	chr13:67575000-67575600	Enhancers	Brain Anterior Caudate	brain
7	chr13:67575000-67575800	Enhancers	Brain Hippocampus Middle	brain
8	chr13:67575400-67576000	Enhancers	A549	lung

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