Variant report

Variant	rs12800896
Chromosome Location	chr11:5734084-5734085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:5621057..5622077-chr11:5733143..5734453,7	MCF-7	breast:
2	chr11:5497160..5498060-chr11:5733696..5734321,2	MCF-7	breast:
3	chr11:5621202..5622094-chr11:5733662..5734343,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10400251	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12099036	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12223005	0.85[EUR][1000 genomes]
rs12224687	0.83[EUR][1000 genomes]
rs12792180	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12792550	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12803433	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12805134	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1603796	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34279421	0.97[ASN][1000 genomes]
rs34464178	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34559010	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34624600	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34734399	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34772298	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34818142	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35257755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35378018	0.97[ASN][1000 genomes]
rs35476279	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35725436	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36092957	1.00[ASN][1000 genomes]
rs36173363	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4457786	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4573706	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66481907	1.00[ASN][1000 genomes]
rs67573252	0.97[ASN][1000 genomes]
rs7128460	0.84[CHB][hapmap]
rs7130646	1.00[ASN][1000 genomes]
rs71490147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71490148	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404224	1.00[ASN][1000 genomes]
rs7936441	0.99[ASN][1000 genomes]
rs7937241	0.93[EUR][1000 genomes];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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12800896	TRIM68	cis	cerebellum	SCAN
rs12800896	C11orf17	cis	parietal	SCAN
rs12800896	OR52N2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5713000-5734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr11:5713600-5734800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:5713600-5745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:5717400-5734400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:5718000-5734600	Weak transcription	HUVEC	blood vessel
6	chr11:5730400-5736000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:5731000-5734200	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:5731000-5741000	Weak transcription	HSMMtube	muscle
9	chr11:5731000-5743800	Weak transcription	Liver	Liver
10	chr11:5731200-5734200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:5731200-5734600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:5731200-5734800	Weak transcription	Lung	lung
13	chr11:5731200-5735200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:5731200-5736400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:5731200-5740600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:5731200-5740600	Weak transcription	Primary B cells from cord blood	blood
17	chr11:5731200-5740600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:5731200-5740600	Weak transcription	Adipose Nuclei	Adipose
19	chr11:5731200-5741000	Weak transcription	Osteobl	bone
20	chr11:5731200-5748000	Weak transcription	Spleen	Spleen
21	chr11:5731200-5748200	Weak transcription	Placenta	Placenta
22	chr11:5731200-5749200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:5731400-5735400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:5731400-5736200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr11:5731600-5734800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:5731600-5737600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:5731800-5734200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:5731800-5734400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:5731800-5742400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:5732400-5742000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:5732400-5742200	Weak transcription	Ovary	ovary
32	chr11:5732400-5743000	Weak transcription	Primary T cells from cord blood	blood
33	chr11:5732400-5750000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:5732600-5742000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:5732600-5743000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr11:5732800-5740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:5732800-5741800	Weak transcription	HSMM	muscle
38	chr11:5733000-5734600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr11:5733000-5734600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:5733000-5735000	Weak transcription	GM12878-XiMat	blood
41	chr11:5733000-5741000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:5733600-5734800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:5733800-5735600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:5733800-5736800	Weak transcription	Monocytes-CD14+_RO01746	blood

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