Variant report

Variant	rs35320690
Chromosome Location	chr3:135932494-135932495
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	chr3:135915739..135918112-chr3:135931092..135933753,3	K562	blood:
2	chr3:135928475..135930111-chr3:135931628..135934340,2	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512990	1.00[CEU][hapmap]
rs11720497	1.00[ASN][1000 genomes]
rs12330335	1.00[CEU][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695645	0.83[AFR][1000 genomes]
rs13068210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13081671	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs13082532	1.00[ASN][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393787	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403763	1.00[CEU][hapmap]
rs28519617	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634226	0.94[GIH][hapmap]
rs28669017	1.00[GIH][hapmap];0.95[LWK][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34324561	0.82[AFR][1000 genomes]
rs34864445	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34913797	0.94[GIH][hapmap]
rs35352346	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs35837273	1.00[ASN][1000 genomes]
rs3905668	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56398805	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769762	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792630	1.00[CEU][hapmap]
rs6793835	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs6799056	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73222243	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9653930	1.00[CEU][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9826454	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9832813	0.81[LWK][hapmap];0.92[MKK][hapmap]
rs9834966	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9837158	0.94[GIH][hapmap];1.00[YRI][hapmap]
rs9844666	0.94[GIH][hapmap]
rs9848926	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9870122	0.80[EUR][1000 genomes]
rs9872178	0.87[AFR][1000 genomes]
rs9880211	0.94[GIH][hapmap];1.00[YRI][hapmap]
rs9881400	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];1.00[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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35320690	MSL2	cis	cerebellum	SCAN
rs35320690	PPP2R3A	cis	cerebellum	SCAN
rs35320690	RNF184	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135930800-135934200	Enhancers	Liver	Liver
2	chr3:135931400-135933400	Enhancers	HepG2	liver

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