Variant report

Variant	rs195579
Chromosome Location	chr2:53475338-53475339
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	chr2:53474174..53476615-chr2:53992818..53995812,2	K562	blood:

Variant related genes	Relation type
ENSG00000115239	Chromatin interaction
ENSG00000143942	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10165023	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10177688	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10188604	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10203900	0.84[EUR][1000 genomes]
rs1118767	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1118768	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1118770	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11903677	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12474297	0.82[EUR][1000 genomes]
rs12620248	0.88[ASN][1000 genomes]
rs13004337	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1344596	0.82[EUR][1000 genomes]
rs1344597	0.82[EUR][1000 genomes]
rs1346002	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1364664	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1364665	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1364667	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1364670	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1364671	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1364672	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1364673	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1424956	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1424992	0.83[EUR][1000 genomes]
rs1424994	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1582670	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1582671	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17044227	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1820324	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1863181	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs195575	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs195578	0.80[ASN][1000 genomes]
rs195580	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195582	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs195583	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs195584	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1965043	0.82[EUR][1000 genomes]
rs2357182	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545324	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728299	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6734586	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6735690	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7561971	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7576422	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7577454	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7593278	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7602663	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7604098	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7607794	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751897	chr2:53358205-53475338	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1013201	chr2:53473426-53553384	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv522095	chr2:53475338-53551600	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	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
rs195579	RTN4	cis	parietal	SCAN
rs195579	PRDXDD1P	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53471800-53480400	Weak transcription	Pancreas	Pancrea
2	chr2:53474800-53476200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:53475000-53476000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:53475000-53479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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