Variant report

Variant	rs3132742
Chromosome Location	chr11:65263001-65263002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64845733..64847412-chr11:65262539..65264597,2	K562	blood:
2	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
3	chr11:65262963..65264911-chr11:65321406..65323614,2	K562	blood:
4	chr11:65116402..65157784-chr11:65261420..65278410,154	K562	blood:
5	chr11:65262109..65269742-chr11:65336183..65344125,16	MCF-7	breast:
6	chr11:65261343..65264179-chr11:65354610..65357170,2	K562	blood:
7	chr11:65262833..65264423-chr11:65305627..65307751,2	K562	blood:
8	chr11:65262283..65263978-chr11:65419665..65421629,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146670	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000173825	Chromatin interaction
ENSG00000255478	Chromatin interaction
ENSG00000162241	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000126391	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1194338	0.83[EUR][1000 genomes]
rs1626021	0.82[AMR][1000 genomes]
rs1784101	0.81[AMR][1000 genomes]
rs1784860	0.80[AMR][1000 genomes]
rs2105608	0.82[AMR][1000 genomes]
rs2957268	0.80[AMR][1000 genomes]
rs2957269	0.81[AMR][1000 genomes]
rs3132767	0.80[AMR][1000 genomes]
rs588298	0.84[AMR][1000 genomes]
rs591291	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs661403	0.82[AMR][1000 genomes]
rs7114809	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
4	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
5	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
6	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
7	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
8	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3132742	NEAT1	cis	Esophagus Muscularis	GTEx
rs3132742	NEAT1	cis	Esophagus Mucosa	GTEx
rs3132742	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs3132742	NEAT1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65252800-65264400	Enhancers	Placenta	Placenta
2	chr11:65252800-65265200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:65253200-65263800	Enhancers	Fetal Thymus	thymus
4	chr11:65253200-65264000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:65253400-65264400	Enhancers	Left Ventricle	heart
6	chr11:65254000-65263800	Enhancers	Right Atrium	heart
7	chr11:65254200-65264200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr11:65254800-65264200	Enhancers	Primary B cells from peripheral blood	blood
9	chr11:65255200-65263600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:65255800-65263400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:65255800-65264200	Enhancers	Fetal Stomach	stomach
12	chr11:65255800-65264200	Enhancers	Stomach Mucosa	stomach
13	chr11:65256000-65263600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:65256000-65264000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr11:65256000-65264000	Enhancers	Fetal Muscle Trunk	muscle
16	chr11:65256000-65264000	Enhancers	Fetal Muscle Leg	muscle
17	chr11:65256000-65265200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:65256200-65263800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:65256200-65265200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:65256600-65263400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:65257000-65263400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:65257600-65263800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:65258400-65263200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:65258800-65264200	Enhancers	Primary hematopoietic stem cells	blood
25	chr11:65259400-65263600	Enhancers	Thymus	Thymus
26	chr11:65259400-65263800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:65259800-65264000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:65259800-65264000	Enhancers	Fetal Heart	heart
29	chr11:65260200-65263800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:65260200-65263800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr11:65260400-65263600	Enhancers	NHDF-Ad	bronchial
32	chr11:65260400-65264000	Enhancers	Primary B cells from cord blood	blood
33	chr11:65260600-65263600	Enhancers	Colon Smooth Muscle	Colon
34	chr11:65260600-65264200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:65260800-65263600	Weak transcription	Fetal Brain Female	brain
36	chr11:65260800-65263800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:65260800-65263800	Enhancers	Brain Cingulate Gyrus	brain
38	chr11:65260800-65263800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr11:65261000-65263600	Enhancers	NHLF	lung
40	chr11:65261000-65264000	Enhancers	Brain Anterior Caudate	brain
41	chr11:65261000-65265200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr11:65261000-65265200	Weak transcription	Gastric	stomach
43	chr11:65261200-65263400	Weak transcription	Lung	lung
44	chr11:65261200-65263800	Weak transcription	Small Intestine	intestine
45	chr11:65261200-65264200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:65261400-65263400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr11:65261400-65263600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:65261400-65263600	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr11:65261400-65263600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:65261400-65263800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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