Variant report

Variant	rs1909262
Chromosome Location	chr11:5424050-5424051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10742678	0.81[CHB][hapmap]
rs10837882	0.90[JPT][hapmap]
rs10838065	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838067	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838092	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs10838093	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs10838094	0.91[CEU][hapmap]
rs10838095	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs11037045	0.89[JPT][hapmap]
rs11037120	0.90[JPT][hapmap]
rs11037350	0.82[ASN][1000 genomes]
rs12281975	0.80[ASN][1000 genomes]
rs1498471	0.94[CEU][hapmap]
rs1498473	0.92[CEU][hapmap]
rs1498492	0.84[CHD][hapmap]
rs2467223	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467224	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467225	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471991	1.00[JPT][hapmap]
rs2471993	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2647547	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs2647548	0.88[CEU][hapmap]
rs2647550	0.88[CEU][hapmap]
rs2647551	0.81[CEU][hapmap]
rs2647552	0.88[CEU][hapmap]
rs2647555	0.88[CEU][hapmap]
rs2647556	0.88[CEU][hapmap]
rs2647558	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647564	0.84[JPT][hapmap]
rs2647565	0.90[JPT][hapmap]
rs2647566	0.87[ASN][1000 genomes]
rs2647570	0.91[CEU][hapmap]
rs2647571	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2647573	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2647574	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2647579	1.00[JPT][hapmap]
rs2647584	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647586	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647588	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647589	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723375	0.88[CEU][hapmap]
rs2723388	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736527	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736531	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736532	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2736538	0.88[CEU][hapmap]
rs2736539	0.88[CEU][hapmap]
rs2736540	0.88[CEU][hapmap]
rs2736579	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2736581	0.87[ASN][1000 genomes]
rs2736586	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2736587	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2736588	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2736590	0.91[CEU][hapmap]
rs2736591	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35392185	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910781	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910787	0.84[ASN][1000 genomes]
rs4910788	0.84[ASN][1000 genomes]
rs7934316	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9795356	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
2	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv896932	chr11:5392484-5424170	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
6	nsv1044243	chr11:5401036-5432316	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
7	nsv896933	chr11:5402315-5440620	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	esv2761646	chr11:5406123-5454241	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	esv1846298	chr11:5410103-5431986	Enhancers Strong transcription Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv430314	chr11:5411744-5496924	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
11	esv2757420	chr11:5416622-5492033	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
12	esv2759800	chr11:5416622-5492033	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1909262	RBMXL2	cis	parietal	SCAN
rs1909262	TRIM5	cis	parietal	SCAN
rs1909262	OR51B2	cis	cerebellum	SCAN
rs1909262	ART1	cis	cerebellum	SCAN
rs1909262	C11orf42	cis	parietal	SCAN
rs1909262	OR51E1	cis	cerebellum	SCAN
rs1909262	KRTAP5-2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5423000-5424200	Weak transcription	K562	blood

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