Variant report

Variant	rs4758427
Chromosome Location	chr11:5834934-5834935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10742793	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742796	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769235	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769236	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769241	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769247	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838637	0.94[ASN][1000 genomes]
rs10838655	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838665	0.89[EUR][1000 genomes]
rs10838666	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838667	0.89[EUR][1000 genomes]
rs11039096	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039102	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039187	0.87[ASN][1000 genomes]
rs11039188	0.87[ASN][1000 genomes]
rs11039193	0.88[ASN][1000 genomes]
rs11607346	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419943	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453415	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453417	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453418	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453419	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453421	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453426	1.00[ASN][1000 genomes]
rs1840175	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343154	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758099	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758101	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758102	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758103	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910849	1.00[ASN][1000 genomes]
rs4910850	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910851	0.86[ASN][1000 genomes]
rs6578689	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925671	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7931236	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937133	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938541	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940624	1.00[ASN][1000 genomes]
rs7940926	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949986	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
14	nsv896952	chr11:5832191-5893376	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4758427	OR52N2	cis	Nerve Tibial	GTEx
rs4758427	OR52N3P	cis	Nerve Tibial	GTEx
rs4758427	OR52N3P	cis	lung	GTEx
rs4758427	OR52N3P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5830800-5836000	Weak transcription	Adipose Nuclei	Adipose
2	chr11:5832000-5835800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr11:5832800-5835200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:5832800-5836000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:5834600-5835200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr11:5834600-5835400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr11:5834600-5838000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr11:5834800-5835400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr11:5834800-5836200	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr11:5834800-5838000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr11:5834800-5838000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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