Variant report

Variant	rs11227226
Chromosome Location	chr11:65330510-65330511
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	CTCF	chr11:65330500-65330650	GM12878	blood:	n/a	n/a
2	CTCF	chr11:65330360-65330510	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65329386..65331502-chr7:29029265..29031276,2	MCF-7	breast:
2	chr11:65195229..65198024-chr11:65329506..65332495,2	K562	blood:
3	chr11:65239690..65241899-chr11:65328225..65330849,2	K562	blood:

Variant related genes	Relation type
LTBP3	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10896017	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227223	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227227	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1144927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12224858	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236684	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4099470	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602922	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs619586	0.82[CHB][hapmap]
rs648578	0.82[CHB][hapmap]
rs664589	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
4	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
5	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
6	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
7	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
8	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
9	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
10	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
11	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
12	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
13	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
14	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
15	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
16	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
17	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
18	nsv897730	chr11:65302893-65376484	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11227226	NEAT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65326600-65332400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:65326800-65334200	Weak transcription	Small Intestine	intestine
3	chr11:65326800-65336800	Weak transcription	Aorta	Aorta
4	chr11:65327200-65332400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:65327400-65331000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:65327400-65331400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:65327600-65330800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:65327600-65331000	Weak transcription	Primary T cells from cord blood	blood
9	chr11:65328000-65332400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:65328200-65331200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:65328400-65330800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr11:65328400-65331000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:65328400-65331000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:65328400-65331200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:65328400-65332800	Weak transcription	Spleen	Spleen
16	chr11:65328400-65333200	Weak transcription	Pancreas	Pancrea
17	chr11:65328400-65333200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:65328600-65331000	Weak transcription	Adipose Nuclei	Adipose
19	chr11:65328600-65336400	Weak transcription	Fetal Brain Female	brain
20	chr11:65328600-65336400	Weak transcription	Gastric	stomach
21	chr11:65328800-65330800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:65328800-65331000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:65328800-65331000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:65328800-65331000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:65328800-65332600	Weak transcription	Hela-S3	cervix
26	chr11:65328800-65332800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:65328800-65333000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:65328800-65333000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:65328800-65333200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:65328800-65333600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:65328800-65333800	Weak transcription	Esophagus	oesophagus
32	chr11:65328800-65334000	Weak transcription	Fetal Intestine Large	intestine
33	chr11:65328800-65334200	Weak transcription	Brain Angular Gyrus	brain
34	chr11:65328800-65334400	Weak transcription	Brain Substantia Nigra	brain
35	chr11:65328800-65335600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:65328800-65335800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:65328800-65336000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:65328800-65336200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr11:65328800-65336200	Weak transcription	Fetal Brain Male	brain
40	chr11:65328800-65336200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:65328800-65336200	Weak transcription	Right Atrium	heart
42	chr11:65328800-65336400	Weak transcription	Left Ventricle	heart
43	chr11:65329000-65330600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:65329000-65330800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:65329000-65330800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:65329000-65330800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:65329000-65330800	Weak transcription	NHDF-Ad	bronchial
48	chr11:65329000-65332000	Weak transcription	Fetal Thymus	thymus
49	chr11:65329000-65332400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:65329000-65332400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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