Variant report

Variant	rs2357180
Chromosome Location	chr2:53417366-53417367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10165023	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10177688	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10188604	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10203900	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11125475	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1118767	0.81[EUR][1000 genomes]
rs1118770	0.82[EUR][1000 genomes]
rs11680194	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11903677	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12471413	0.80[ASN][1000 genomes]
rs12474297	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12616626	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12617583	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620248	0.82[ASN][1000 genomes]
rs13004337	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13006851	0.93[ASN][1000 genomes]
rs1344596	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1344597	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345998	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1345999	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1346000	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1346002	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1364664	0.82[ASN][1000 genomes]
rs1364665	0.81[ASN][1000 genomes]
rs1364667	0.82[ASN][1000 genomes]
rs1364670	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1364671	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1364672	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1364673	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1424956	0.81[ASN][1000 genomes]
rs1424982	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1424991	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1424992	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1424993	0.93[ASN][1000 genomes]
rs1424994	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1559630	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1559632	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1582670	0.82[EUR][1000 genomes]
rs17044227	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1820324	0.82[ASN][1000 genomes]
rs1863181	0.87[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs195579	0.83[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.89[MEX][hapmap]
rs1965043	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2357179	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357182	0.82[ASN][1000 genomes]
rs4672248	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5000352	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545324	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6728299	0.82[ASN][1000 genomes]
rs6734586	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6735690	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7561971	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7563775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7568050	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7576422	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7577454	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7582311	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7593278	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7602663	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7604098	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7607794	0.81[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	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2751897	chr2:53358205-53475338	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1011032	chr2:53384170-53433055	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2357180	CHAC2	cis	cerebellum	SCAN
rs2357180	PRDXDD1P	cis	cerebellum	SCAN
rs2357180	CCDC104	cis	parietal	SCAN
rs2357180	RTN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53414800-53417400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:53414800-53417600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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