Variant report

Variant	rs39396
Chromosome Location	chr7:103489875-103489876
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	chr7:103487611..103490100-chr7:103622527..103624433,2	K562	blood:
2	chr7:103483125..103487990-chr7:103488030..103491308,6	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10278412	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12538149	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3886303	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3908281	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39352	0.98[EUR][1000 genomes]
rs39353	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]
rs39354	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs39355	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs39356	1.00[CEU][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39357	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs39358	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39359	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs39360	1.00[CEU][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39362	1.00[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs39363	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39364	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39365	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs39366	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39367	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39368	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs39370	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs39371	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39372	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39374	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39375	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39377	0.80[EUR][1000 genomes]
rs39378	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs39380	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39382	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39383	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39384	1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39385	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39388	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39390	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs39391	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39393	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39399	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs39400	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39403	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39404	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39406	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4727576	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4729935	0.84[EUR][1000 genomes]
rs6465939	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6465942	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6944760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6960198	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7784621	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9986961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1030128	chr7:103489028-103517045	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs39396	PILRA	cis	parietal	SCAN
rs39396	DNAJC2	cis	cerebellum	SCAN
rs39396	ORAI2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103473200-103495200	Weak transcription	HepG2	liver
2	chr7:103486000-103497800	Weak transcription	K562	blood

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