Variant report

Variant	rs6547119
Chromosome Location	chr2:77274083-77274084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10186823	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713890	0.83[CEU][hapmap];0.91[GIH][hapmap]
rs13033902	0.84[CEU][hapmap];0.91[GIH][hapmap];0.94[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs13034088	0.84[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes]
rs13397044	0.90[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13430336	0.88[CHB][hapmap]
rs1348825	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1374394	0.97[GIH][hapmap]
rs1446689	0.94[CEU][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs1446690	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs1446694	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1446717	0.97[GIH][hapmap];0.85[MEX][hapmap]
rs1446718	0.91[GIH][hapmap]
rs1542187	0.89[GIH][hapmap]
rs17013615	0.94[GIH][hapmap];0.85[MEX][hapmap]
rs17040500	0.97[GIH][hapmap];0.89[MEX][hapmap]
rs17089	1.00[GIH][hapmap];0.90[MEX][hapmap]
rs1867891	0.94[CHB][hapmap]
rs1900342	0.94[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982341	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs4510248	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6547106	0.86[GIH][hapmap]
rs6750979	0.81[GIH][hapmap]
rs6754347	1.00[CEU][hapmap]
rs7561189	0.91[GIH][hapmap]
rs7595678	0.89[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.85[EUR][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	nsv834266	chr2:77120236-77287504	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv997284	chr2:77233426-77303198	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1014895	chr2:77263452-77414507	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv874331	chr2:77264354-77305123	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6547119	SMYD5	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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