Variant report

Variant	rs6479670
Chromosome Location	chr10:61697498-61697499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:61697187..61699091-chr10:61700833..61702353,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1008887	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10740000	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10994030	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs10994081	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10994083	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1149660	0.85[GIH][hapmap]
rs1171847	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1171849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1184593	0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1664275	0.90[ASN][1000 genomes]
rs1684913	0.84[ASN][1000 genomes]
rs1709342	0.85[GIH][hapmap];0.88[TSI][hapmap]
rs2034200	0.91[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3099370	0.90[ASN][1000 genomes]
rs3099371	0.90[ASN][1000 genomes]
rs3851249	0.81[MEX][hapmap]
rs3910925	0.81[CHD][hapmap]
rs6479653	0.82[GIH][hapmap]
rs6479673	0.93[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479675	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073136	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7893603	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897677	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7910256	0.85[GIH][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479670	EGR2	cis	parietal	SCAN
rs6479670	CCDC6	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61696600-61698200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr10:61696600-61698200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr10:61696800-61697600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr10:61696800-61698000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr10:61697200-61697600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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