Variant report

Variant	rs858671
Chromosome Location	chr17:45271680-45271681
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1102461	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079756	0.80[ASN][1000 genomes]
rs11079762	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11079763	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1634269	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs221596	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221603	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221604	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs221605	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs221607	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2678693	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs4968308	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504743	0.82[ASN][1000 genomes]
rs6504744	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8073936	0.85[ASN][1000 genomes]
rs858675	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858680	0.86[ASN][1000 genomes]
rs9747171	0.85[ASN][1000 genomes]
rs9894365	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs858671	DBF4B	cis	parietal	SCAN
rs858671	KRT9	cis	parietal	SCAN
rs858671	TUBG1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45266800-45277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:45267200-45275000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:45267200-45277200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:45268400-45281000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr17:45270600-45274800	Weak transcription	HSMM	muscle
6	chr17:45270600-45281200	Weak transcription	Spleen	Spleen
7	chr17:45270800-45274800	Weak transcription	HSMMtube	muscle
8	chr17:45270800-45276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:45270800-45277200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:45271600-45272200	Enhancers	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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