Variant report

Variant	rs4993442
Chromosome Location	chr22:30253256-30253257
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1071888	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076137	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12168552	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537	0.80[CEU][hapmap]
rs131278	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.90[YRI][hapmap]
rs131291	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.90[YRI][hapmap]
rs131296	0.87[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs140105	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs140108	0.82[CEU][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs140135	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs140151	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17643918	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807509	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs193481	0.80[EUR][1000 genomes]
rs2017677	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051764	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2105870	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2349225	0.91[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs2412960	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412963	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249400	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28257	0.81[EUR][1000 genomes]
rs34862234	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35705048	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36578	0.88[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36580	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36590	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36591	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36594	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36596	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36598	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36600	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36601	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36605	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36606	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36607	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788423	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3887275	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3958025	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39712	0.89[EUR][1000 genomes]
rs41162	0.82[ASW][hapmap];0.95[CEU][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs41164	0.91[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs41172	0.82[ASW][hapmap];0.83[CEU][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs41174	0.86[CEU][hapmap]
rs41175	0.81[EUR][1000 genomes]
rs4239932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820820	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4820822	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4823055	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4823063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752968	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752986	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752988	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5752993	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763630	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763634	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763644	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763674	0.87[EUR][1000 genomes]
rs5763675	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763680	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763689	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs715523	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7286070	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7292615	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737904	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs737909	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737912	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8136147	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8139994	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8141680	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9620926	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625873	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625874	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625878	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625879	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1851082	chr22:30253256-30294744	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4993442	NEFH	cis	cerebellum	SCAN
rs4993442	CRYBB3	cis	parietal	SCAN
rs4993442	TTC28	cis	cerebellum	SCAN
rs4993442	KIAA1671	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30248400-30254600	Weak transcription	HSMMtube	muscle
2	chr22:30253000-30255200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30253000-30257200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr22:30253000-30257200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr22:30253200-30255200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr22:30253200-30255200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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