Variant report

Variant	rs5997546
Chromosome Location	chr22:30259342-30259343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1076135	0.85[CEU][hapmap]
rs12710565	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140124	0.81[CEU][hapmap]
rs140145	0.85[CEU][hapmap]
rs140147	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs140149	0.85[CEU][hapmap]
rs1807508	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1807513	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007446	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs2007458	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074706	0.81[CEU][hapmap]
rs2074707	0.81[CEU][hapmap]
rs2189802	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301402	0.85[CEU][hapmap]
rs3747149	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3747150	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3788420	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3958027	0.81[EUR][1000 genomes]
rs41159	0.81[EUR][1000 genomes]
rs41165	1.00[CEU][hapmap]
rs41168	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs41171	0.92[CEU][hapmap]
rs41173	0.92[CEU][hapmap]
rs4630869	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820824	0.84[ASN][1000 genomes]
rs55805200	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752964	0.81[CEU][hapmap]
rs5752973	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752975	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752978	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs5752992	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763512	0.81[CEU][hapmap]
rs5763559	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763565	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763581	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763589	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5763591	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763614	0.82[EUR][1000 genomes]
rs5763638	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763645	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763646	0.83[ASN][1000 genomes]
rs5763649	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763650	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763651	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763671	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763688	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5997530	0.81[CEU][hapmap]
rs5997549	0.90[EUR][1000 genomes]
rs6006288	0.90[EUR][1000 genomes]
rs6006300	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713656	0.85[CEU][hapmap]
rs713657	0.81[CEU][hapmap]
rs7289604	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737908	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs737911	0.89[CEU][hapmap]
rs737939	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs740041	0.81[CEU][hapmap]
rs9306465	0.85[CEU][hapmap]
rs9306468	0.92[CEU][hapmap]
rs960987	0.81[EUR][1000 genomes]
rs9614077	0.81[EUR][1000 genomes]
rs9614100	0.80[EUR][1000 genomes]
rs997913	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5997546	NEFH	cis	cerebellum	SCAN
rs5997546	ASCC2	cis	cerebellum	SCAN
rs5997546	LIF	cis	parietal	SCAN
rs5997546	CRYBB3	cis	parietal	SCAN
rs5997546	TTC28	cis	cerebellum	SCAN
rs5997546	MTMR3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30257600-30260800	Weak transcription	HepG2	liver
2	chr22:30258200-30267600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30258400-30263200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr22:30258400-30263400	Weak transcription	Fetal Heart	heart
5	chr22:30258400-30263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr22:30259200-30259400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr22:30259200-30259800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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