Variant report

Variant	rs195583
Chromosome Location	chr2:53479450-53479451
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10165023	0.82[ASN][1000 genomes]
rs10177688	0.80[ASN][1000 genomes]
rs10188604	0.82[ASN][1000 genomes]
rs1118767	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1118768	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1118770	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11903677	0.82[ASN][1000 genomes]
rs12620248	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004337	0.82[ASN][1000 genomes]
rs13006851	0.82[EUR][1000 genomes]
rs1346002	0.82[ASN][1000 genomes]
rs1364664	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1364665	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1364667	0.86[ASN][1000 genomes]
rs1364670	0.84[ASN][1000 genomes]
rs1364671	0.82[ASN][1000 genomes]
rs1364672	0.82[ASN][1000 genomes]
rs1424956	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1424993	0.82[EUR][1000 genomes]
rs1424994	0.81[ASN][1000 genomes]
rs1582670	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1582671	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1820324	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1863181	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs195575	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs195579	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs195580	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs195582	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195584	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357182	0.86[ASN][1000 genomes]
rs6545324	0.82[ASN][1000 genomes]
rs6728299	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6734586	0.82[ASN][1000 genomes]
rs6735690	0.82[ASN][1000 genomes]
rs7561971	0.82[ASN][1000 genomes]
rs7576422	0.83[ASN][1000 genomes]
rs7577454	0.82[ASN][1000 genomes]
rs7602663	0.82[ASN][1000 genomes]
rs7604098	0.82[ASN][1000 genomes]
rs7607794	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1013201	chr2:53473426-53553384	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv522095	chr2:53475338-53551600	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv522463	chr2:53475338-53551600	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs195583	PRDXDD1P	cis	cerebellum	SCAN
rs195583	RTN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53471800-53480400	Weak transcription	Pancreas	Pancrea
2	chr2:53477200-53480000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:53479000-53479600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:53479000-53479600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:53479000-53479600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr2:53479000-53479600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr2:53479000-53479800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:53479200-53479600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:53479200-53480200	Enhancers	Hela-S3	cervix

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