Variant report

Variant	rs1784860
Chromosome Location	chr11:65240712-65240713
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65239862..65242491-chr11:65290077..65292904,5	K562	blood:
2	chr11:65138209..65140273-chr11:65239128..65241917,2	K562	blood:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
4	chr11:65120513..65124729-chr11:65238315..65241073,4	K562	blood:
5	chr11:65239690..65241899-chr11:65328225..65330849,2	K562	blood:
6	chr11:65238018..65240759-chr11:65336079..65337940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260233	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000173825	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000173465	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10896001	0.83[AMR][1000 genomes]
rs11227204	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1616810	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1621277	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626021	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1784100	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1784101	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784858	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1784859	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105608	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508711	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2508712	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2846861	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957268	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957269	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015965	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3015966	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3016343	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3132742	0.80[AMR][1000 genomes]
rs3132743	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3132767	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587080	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs587390	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588298	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs591291	0.84[AMR][1000 genomes]
rs602838	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs604676	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605035	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs660588	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs661403	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs682845	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7114809	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7934628	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic 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	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong 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	474 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1784860	NEAT1	cis	Nerve Tibial	GTEx
rs1784860	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs1784860	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs1784860	NEAT1	cis	Esophagus Muscularis	GTEx
rs1784860	NEAT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65223200-65244000	Weak transcription	Fetal Kidney	kidney
2	chr11:65234000-65244000	Weak transcription	Fetal Brain Female	brain
3	chr11:65237800-65241000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:65237800-65241000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:65237800-65241200	Flanking Active TSS	Hela-S3	cervix
6	chr11:65238200-65241000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:65238600-65241400	Enhancers	Placenta	Placenta
8	chr11:65238800-65240800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr11:65238800-65240800	Enhancers	Fetal Intestine Small	intestine
10	chr11:65238800-65240800	Enhancers	Fetal Muscle Trunk	muscle
11	chr11:65238800-65241000	Enhancers	Primary B cells from peripheral blood	blood
12	chr11:65238800-65241400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:65239400-65243800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:65239400-65243800	Weak transcription	Liver	Liver
15	chr11:65239400-65243800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:65239400-65244000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:65239600-65240800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:65239600-65240800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr11:65239600-65241000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:65239600-65241000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr11:65239600-65241000	Enhancers	Primary B cells from cord blood	blood
22	chr11:65239600-65241000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr11:65239600-65241000	Enhancers	HUVEC	blood vessel
24	chr11:65239600-65241200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:65239600-65241400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:65239600-65241600	Enhancers	Primary hematopoietic stem cells	blood
27	chr11:65239600-65241800	Weak transcription	Psoas Muscle	Psoas
28	chr11:65239600-65243800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:65239600-65243800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:65239600-65243800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:65239600-65243800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:65239600-65243800	Weak transcription	Brain Substantia Nigra	brain
33	chr11:65239600-65243800	Weak transcription	Colonic Mucosa	Colon
34	chr11:65239600-65243800	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:65239600-65243800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:65239600-65243800	Weak transcription	Esophagus	oesophagus
37	chr11:65239600-65243800	Weak transcription	Pancreas	Pancrea
38	chr11:65239600-65243800	Weak transcription	Right Ventricle	heart
39	chr11:65239600-65243800	Weak transcription	Small Intestine	intestine
40	chr11:65239600-65244000	Weak transcription	Brain Angular Gyrus	brain
41	chr11:65239600-65244400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr11:65239800-65240800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:65239800-65241000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr11:65239800-65242400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:65239800-65243600	Weak transcription	Spleen	Spleen
46	chr11:65239800-65243800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:65239800-65243800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:65239800-65243800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:65239800-65243800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:65239800-65243800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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