Variant report

Variant	rs13417129
Chromosome Location	chr2:35010043-35010044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10169709	0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10171796	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10172221	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10175096	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10175564	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12479367	1.00[ASN][1000 genomes]
rs13395024	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015668	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015690	1.00[ASN][1000 genomes]
rs17015696	1.00[ASN][1000 genomes]
rs17261035	1.00[ASN][1000 genomes]
rs17261049	1.00[ASN][1000 genomes]
rs2371734	1.00[ASN][1000 genomes]
rs280700	1.00[ASN][1000 genomes]
rs280701	1.00[ASN][1000 genomes]
rs280707	1.00[ASN][1000 genomes]
rs280714	1.00[ASN][1000 genomes]
rs3748925	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57364378	1.00[ASN][1000 genomes]
rs59065684	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59618150	1.00[ASN][1000 genomes]
rs6741489	1.00[ASN][1000 genomes]
rs67565342	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796906	1.00[ASN][1000 genomes]
rs72860441	1.00[ASN][1000 genomes]
rs72860499	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7573294	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941551	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941670	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873804	chr2:34156867-35047107	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv873810	chr2:34456200-35047107	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv873821	chr2:34738616-35416075	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1003361	chr2:34746445-35202302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873825	chr2:34892832-35115848	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1003322	chr2:34898412-35216795	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv581375	chr2:34912850-35032910	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
8	nsv873828	chr2:34919515-35022419	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1010863	chr2:34922329-35052108	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
10	nsv1002915	chr2:34923003-35052108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
11	nsv873829	chr2:34928080-35022419	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
12	nsv430679	chr2:34946679-35025804	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	nsv1003970	chr2:34956712-35013666	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv1008947	chr2:34959421-35019746	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	nsv581384	chr2:34965789-35013851	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv873830	chr2:34972791-35047107	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv1008320	chr2:34982747-35010043	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	nsv1003857	chr2:34986833-35010043	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv1002310	chr2:34986833-35019746	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv524038	chr2:34990937-35073607	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13417129	PRKD3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:35010000-35010400	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr2:35010000-35010400	Enhancers	Brain Substantia Nigra	brain

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