Variant report

Variant	rs39353
Chromosome Location	chr7:103468343-103468344
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:55884808..55887804-chr7:103468057..103471037,2	MCF-7	breast:
2	chr7:103455999..103458668-chr7:103467643..103469823,2	K562	blood:
3	chr7:103467206..103468826-chr7:103482510..103485701,3	K562	blood:
4	chr7:103466010..103468744-chr7:103470404..103473260,3	K562	blood:

Variant related genes	Relation type
ENSG00000252064	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10278412	0.83[EUR][1000 genomes]
rs3886303	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs3908281	0.85[EUR][1000 genomes]
rs39350	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs39352	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39357	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39359	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39361	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs39362	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39365	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39366	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39369	0.83[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39370	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39371	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39373	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs39374	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39378	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39383	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39388	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39390	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39391	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39393	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39396	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39398	1.00[CEU][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs39399	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39400	1.00[CEU][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes]
rs39403	0.94[EUR][1000 genomes]
rs39404	0.94[EUR][1000 genomes]
rs39406	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4727576	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4729935	0.83[EUR][1000 genomes]
rs6465939	0.82[EUR][1000 genomes]
rs6465942	0.87[EUR][1000 genomes]
rs6944760	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6960198	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7784621	0.88[EUR][1000 genomes]
rs9986961	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1843940	chr7:103421702-103590285	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv523031	chr7:103457789-103470499	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv934055	chr7:103462527-103473944	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs39353	PILRA	cis	parietal	SCAN
rs39353	ORAI2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103457800-103472000	Weak transcription	HepG2	liver
2	chr7:103461200-103482400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:103466600-103481800	Weak transcription	K562	blood

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