Variant report

Variant	rs1664278
Chromosome Location	chr10:61694304-61694305
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:61694085..61696780-chr10:61751224..61753093,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1171833	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1183347	0.95[EUR][1000 genomes]
rs12572828	0.85[EUR][1000 genomes]
rs12573055	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12763583	0.94[ASN][1000 genomes]
rs12776024	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[ASN][1000 genomes]
rs1624715	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1664254	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1664257	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1664258	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1664260	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs1664262	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1664276	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1664279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684898	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1684900	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1684902	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1684904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972950	0.88[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2166270	0.94[ASN][1000 genomes]
rs2166271	0.94[ASN][1000 genomes]
rs2440906	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2440910	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs2440916	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450463	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450464	0.86[EUR][1000 genomes]
rs2450468	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs3763745	0.82[MEX][hapmap]
rs4948249	0.80[CEU][hapmap]
rs56221953	0.86[EUR][1000 genomes]
rs895243	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]

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	esv1800316	chr10:61639599-61700473	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1664278	SLC16A9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61694200-61695600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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