Variant report

Variant	rs1453415
Chromosome Location	chr11:5829019-5829020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10734554	0.83[GIH][hapmap]
rs10742787	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs10742788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs10742789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs10742793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742796	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769224	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs10769232	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs10769235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769241	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769247	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838637	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs10838648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs10838655	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838665	0.88[EUR][1000 genomes]
rs10838666	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838667	0.88[EUR][1000 genomes]
rs11039096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039140	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039187	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11039188	0.84[ASN][1000 genomes]
rs11039193	0.86[ASN][1000 genomes]
rs11607346	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419943	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1377512	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453421	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453424	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs1453426	0.98[ASN][1000 genomes]
rs1840175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2343154	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4758101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758102	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758103	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758113	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs4758427	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4910849	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910850	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910851	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs6578689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924824	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7925671	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7931236	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7935300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7937133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7938541	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7940624	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7940926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949986	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	nsv553277	chr11:5722948-6010075	Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv1843296	chr11:5730377-5970717	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv2758255	chr11:5730377-5970717	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv2759801	chr11:5730377-6007613	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv832058	chr11:5747594-5926814	Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
13	nsv896951	chr11:5773981-5832191	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv2757421	chr11:5776623-5842356	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv1041196	chr11:5790800-5829039	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1837262	chr11:5808353-5830288	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1453415	OR52N3P	cis	lung	GTEx
rs1453415	OR51B5	cis	parietal	SCAN
rs1453415	OR52N3P	cis	Adipose Subcutaneous	GTEx
rs1453415	OR52N3P	cis	Artery Tibial	GTEx
rs1453415	TRIM22	cis	parietal	SCAN
rs1453415	OR52N2	cis	Nerve Tibial	GTEx
rs1453415	ASCL2	cis	parietal	SCAN
rs1453415	OR52N3P	cis	Nerve Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5823200-5829600	Weak transcription	Fetal Heart	heart
2	chr11:5825800-5829400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:5828800-5829200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:5828800-5829200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr11:5828800-5829600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr11:5828800-5829800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr11:5828800-5829800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:5828800-5829800	Enhancers	Placenta	Placenta
9	chr11:5828800-5832200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:5829000-5829200	Enhancers	Right Atrium	heart
11	chr11:5829000-5829200	Active TSS	Right Ventricle	heart
12	chr11:5829000-5829600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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