Variant report

Variant	rs11038833
Chromosome Location	chr11:5739512-5739513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:5739017-5740020	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:5714465-5718134..11:5736363-5740069	GM12878	blood:
2	11:5700314-5707362..11:5736363-5740069	GM12878	blood:
3	11:5218976-5222789..11:5736363-5740069	H1-hESC	embryonic stem cell:	embryo
4	11:4778081-4789138..11:5736363-5740069	Hela-S3	cervix:
5	11:5250847-5268367..11:5736363-5740069	H1-hESC	embryonic stem cell:	embryo
6	11:5243048-5250847..11:5736363-5740069	GM12878	blood:

Variant related genes	Relation type
OR52U1P	TF binding region
ENSG00000176742	Chromatin interaction
ENSG00000132256	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000221031	Chromatin interaction
ENSG00000260629	Chromatin interaction
ENSG00000229988	Chromatin interaction
ENSG00000244734	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000167346	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10838576	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038820	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038821	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11038825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038832	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11038858	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038859	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12224433	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12285602	0.86[MEX][hapmap]
rs1391640	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498562	1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs61181515	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6578680	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7129530	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7396766	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs7482762	0.94[ASN][1000 genomes]
rs883983	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9665780	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5713600-5745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:5731000-5741000	Weak transcription	HSMMtube	muscle
3	chr11:5731000-5743800	Weak transcription	Liver	Liver
4	chr11:5731200-5740600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:5731200-5740600	Weak transcription	Primary B cells from cord blood	blood
6	chr11:5731200-5740600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:5731200-5740600	Weak transcription	Adipose Nuclei	Adipose
8	chr11:5731200-5741000	Weak transcription	Osteobl	bone
9	chr11:5731200-5748000	Weak transcription	Spleen	Spleen
10	chr11:5731200-5748200	Weak transcription	Placenta	Placenta
11	chr11:5731200-5749200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:5731800-5742400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:5732400-5742000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr11:5732400-5742200	Weak transcription	Ovary	ovary
15	chr11:5732400-5743000	Weak transcription	Primary T cells from cord blood	blood
16	chr11:5732400-5750000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:5732600-5742000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:5732600-5743000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:5732800-5740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:5732800-5741800	Weak transcription	HSMM	muscle
21	chr11:5733000-5741000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:5734400-5740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:5735400-5740800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:5735400-5741000	Weak transcription	Lung	lung
25	chr11:5735400-5742200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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