Variant report

Variant	rs17346310
Chromosome Location	chr9:100649533-100649534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100649531..100652518-chr9:100653450..100655843,2	MCF-7	breast:
2	chr9:100648546..100652838-chr9:100654754..100658082,3	K562	blood:
3	chr9:100641121..100643077-chr9:100648221..100651818,3	MCF-7	breast:
4	chr9:100648000..100649701-chr9:100650318..100652394,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10984193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984297	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10984349	0.90[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs10984462	0.90[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1127703	0.90[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12235434	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12236440	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12237296	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3780416	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3780417	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3780418	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3780419	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4560904	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4618817	0.90[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs62574034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62574035	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67500034	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67975003	0.83[EUR][1000 genomes]
rs68112593	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7025609	0.90[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs7040232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72753548	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72753572	0.83[EUR][1000 genomes]
rs7855917	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864655	0.83[EUR][1000 genomes]
rs7870125	0.86[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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17346310	HIATL1	cis	cerebellum	SCAN
rs17346310	Hs.43687	cis	multi-tissue	Pritchard
rs17346310	C9orf156	cis	multi-tissue	Pritchard
rs17346310	SEC61B	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100637600-100658000	Weak transcription	Gastric	stomach
2	chr9:100637800-100652800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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