Variant report

Variant	rs11227223
Chromosome Location	chr11:65324276-65324277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65323344-65324298	HepG2	liver:	n/a	n/a
2	ELF1	chr11:65324042-65324337	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:65324042-65324322	K562	blood:	n/a	n/a
4	RCOR1	chr11:65322901-65324417	IMR90	lung:	n/a	n/a
5	POLR2A	chr11:65323917-65324404	HCT-116	colon:	n/a	n/a
6	MAZ	chr11:65323932-65326942	IMR90	lung:	n/a	chr11:65326583-65326593 chr11:65325980-65325990

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65322830..65325559-chr11:65385179..65389892,4	K562	blood:
2	chr11:65186486..65188182-chr11:65323386..65325229,2	MCF-7	breast:
3	chr11:65188903..65194388-chr11:65323256..65328284,10	MCF-7	breast:
4	chr11:65322009..65324491-chr11:65418105..65419642,2	MCF-7	breast:
5	chr11:65152331..65154319-chr11:65322563..65324840,2	K562	blood:
6	chr11:65265516..65268533-chr11:65323156..65327547,5	MCF-7	breast:
7	chr11:65322433..65324295-chr11:65381910..65384762,2	MCF-7	breast:
8	chr11:65322271..65324751-chr6:27776572..27778307,2	MCF-7	breast:
9	chr11:65189010..65195293-chr11:65321323..65327708,15	K562	blood:
10	chr11:65269130..65271131-chr11:65323511..65325144,2	MCF-7	breast:
11	chr11:65264952..65268870-chr11:65322730..65327860,7	K562	blood:
12	chr11:65264479..65268560-chr11:65318003..65330456,22	MCF-7	breast:
13	chr11:65123264..65125729-chr11:65322609..65324877,2	K562	blood:
14	chr11:65184371..65196984-chr11:65316952..65328208,29	K562	blood:

No data

Variant related genes	Relation type
LTBP3	TF binding region
ENSG00000245532	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000126391	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10896017	0.83[EUR][1000 genomes]
rs11227226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227227	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12224858	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236684	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4099470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602922	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]

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
rs11227223	NEAT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65318600-65325800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:65318800-65324600	Enhancers	Primary hematopoietic stem cells	blood
3	chr11:65319000-65324600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr11:65319000-65324600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:65320000-65325000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:65320400-65324600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:65320400-65324600	Enhancers	Fetal Intestine Large	intestine
8	chr11:65320800-65324800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:65321200-65324600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:65321200-65324800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr11:65321200-65325400	Enhancers	Fetal Brain Male	brain
12	chr11:65321200-65326200	Enhancers	Spleen	Spleen
13	chr11:65321400-65324600	Enhancers	Placenta	Placenta
14	chr11:65321400-65324800	Enhancers	Esophagus	oesophagus
15	chr11:65321600-65324400	Genic enhancers	Fetal Stomach	stomach
16	chr11:65321600-65324800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:65321800-65324600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:65321800-65324600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:65321800-65324800	Enhancers	K562	blood
20	chr11:65321800-65325000	Enhancers	Stomach Mucosa	stomach
21	chr11:65322000-65324400	Enhancers	HUVEC	blood vessel
22	chr11:65322000-65324400	Enhancers	NHDF-Ad	bronchial
23	chr11:65322000-65324600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:65322200-65324400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:65322200-65324600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:65322200-65324600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:65322200-65325000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr11:65322400-65324400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr11:65322400-65324400	Enhancers	Brain Cingulate Gyrus	brain
30	chr11:65322400-65324600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr11:65322400-65324800	Enhancers	Pancreas	Pancrea
32	chr11:65322600-65324400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:65322600-65324400	Enhancers	Duodenum Mucosa	Duodenum
34	chr11:65322600-65324600	Enhancers	Liver	Liver
35	chr11:65322600-65324600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:65322600-65324800	Enhancers	Left Ventricle	heart
37	chr11:65322600-65325000	Flanking Active TSS	Hela-S3	cervix
38	chr11:65322800-65324400	Enhancers	Primary T cells from cord blood	blood
39	chr11:65322800-65324400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr11:65322800-65324400	Enhancers	Ovary	ovary
41	chr11:65322800-65324400	Flanking Active TSS	Osteobl	bone
42	chr11:65322800-65324800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr11:65322800-65324800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:65322800-65324800	Enhancers	NHEK	skin
45	chr11:65323000-65324400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:65323000-65324400	Enhancers	Right Atrium	heart
47	chr11:65323000-65324600	Weak transcription	Dnd41	blood
48	chr11:65323000-65325000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr11:65323000-65325200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:65323200-65324600	Enhancers	Fetal Heart	heart

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