Variant report

Variant	rs7966829
Chromosome Location	chr12:48615603-48615604
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1061986	0.81[EUR][1000 genomes]
rs10875753	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs10875763	0.83[ASN][1000 genomes]
rs1107654	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168428	1.00[CHD][hapmap];0.86[GIH][hapmap]
rs11168437	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs11168460	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168464	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168474	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168484	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828309	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829841	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387259	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1387260	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1476607	1.00[CHD][hapmap];0.86[GIH][hapmap]
rs1542707	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552550	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054905	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409003	0.85[EUR][1000 genomes]
rs2409004	0.85[EUR][1000 genomes]
rs2450994	0.80[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2468943	0.88[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs2634676	0.81[EUR][1000 genomes]
rs2634678	0.81[EUR][1000 genomes]
rs2634680	0.81[EUR][1000 genomes]
rs2634681	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2634682	0.82[EUR][1000 genomes]
rs2634684	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2634686	0.85[EUR][1000 genomes]
rs2634688	0.82[EUR][1000 genomes]
rs2634689	0.83[EUR][1000 genomes]
rs2634691	0.86[EUR][1000 genomes]
rs2634692	0.86[EUR][1000 genomes]
rs2634693	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2634694	0.85[EUR][1000 genomes]
rs2634697	1.00[ASN][1000 genomes]
rs2732441	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2732445	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732448	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2732453	0.85[EUR][1000 genomes]
rs2732454	0.85[EUR][1000 genomes]
rs2732457	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2732461	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732462	0.90[EUR][1000 genomes]
rs2732466	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2732479	0.81[EUR][1000 genomes]
rs2732480	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs2732481	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2732484	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2732486	0.81[EUR][1000 genomes]
rs2956703	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2956710	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087716	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34286639	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580650	0.83[GIH][hapmap]
rs6580662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297824	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301003	1.00[CHD][hapmap];0.86[GIH][hapmap]
rs7307566	0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315820	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486941	1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs7487682	1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap]
rs7959684	1.00[CHD][hapmap]
rs7975632	0.83[GIH][hapmap]
rs8716	1.00[CHD][hapmap];0.86[GIH][hapmap]
rs923397	0.80[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7966829	TMBIM6	cis	cerebellum	SCAN
rs7966829	H1FNT	cis	Muscle Skeletal	GTEx
rs7966829	ZNF641	cis	cerebellum	SCAN
rs7966829	FKBP11	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48612000-48629600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr12:48612200-48635600	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:48615400-48615800	Enhancers	Rectal Smooth Muscle	rectum
4	chr12:48615600-48619600	Strong transcription	Primary monocytes fromperipheralblood	blood

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