Variant report

Variant	rs1784858
Chromosome Location	chr11:65222952-65222953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65122004..65123879-chr11:65220475..65223059,2	K562	blood:
2	chr11:62608095..62609669-chr11:65220631..65223111,2	MCF-7	breast:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
4	chr11:65222766..65224621-chr11:65305015..65306605,2	K562	blood:
5	chr11:65222762..65225438-chr11:65341182..65342717,2	K562	blood:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000173825	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10896001	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11227204	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11822111	0.83[AMR][1000 genomes]
rs1616810	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1621277	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1626021	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1784100	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1784101	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784859	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784860	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105608	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2508711	0.86[ASN][1000 genomes]
rs2508712	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2846861	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957268	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957269	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015965	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015966	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3016343	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132743	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3132767	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs587080	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587390	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs588298	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs602838	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs604676	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs605035	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs660588	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs661403	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs682845	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7114809	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934628	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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
rs1784858	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs1784858	NEAT1	cis	Muscle Skeletal	GTEx
rs1784858	NEAT1	cis	Esophagus Mucosa	GTEx
rs1784858	NEAT1	cis	Adipose Subcutaneous	GTEx
rs1784858	NEAT1	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65220400-65227000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:65221800-65223200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:65221800-65223200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:65221800-65223200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr11:65221800-65223200	Flanking Active TSS	HSMM	muscle
6	chr11:65221800-65223200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr11:65221800-65225400	Active TSS	GM12878-XiMat	blood
8	chr11:65222000-65223000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr11:65222000-65223000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr11:65222000-65223000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr11:65222000-65223000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr11:65222000-65223000	Active TSS	Brain Germinal Matrix	brain
13	chr11:65222000-65223000	Flanking Active TSS	HUVEC	blood vessel
14	chr11:65222000-65223000	Flanking Active TSS	NHEK	skin
15	chr11:65222000-65223200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:65222000-65223200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr11:65222000-65223200	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr11:65222000-65223200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:65222000-65223200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr11:65222000-65223200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:65222000-65223200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:65222000-65223200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr11:65222000-65223200	Active TSS	Brain Angular Gyrus	brain
24	chr11:65222000-65223200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:65222000-65223200	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr11:65222000-65223200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr11:65222000-65223200	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr11:65222000-65223200	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr11:65222000-65223200	Flanking Active TSS	Fetal Thymus	thymus
30	chr11:65222000-65223200	Flanking Active TSS	Right Atrium	heart
31	chr11:65222000-65223200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr11:65222000-65223200	Flanking Active TSS	Dnd41	blood
33	chr11:65222000-65223200	Flanking Active TSS	NH-A	brain
34	chr11:65222000-65223200	Flanking Active TSS	NHDF-Ad	bronchial
35	chr11:65222000-65224000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:65222200-65223000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr11:65222200-65223000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:65222200-65223000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:65222200-65223000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:65222200-65223000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:65222200-65223000	Flanking Active TSS	Pancreas	Pancrea
42	chr11:65222200-65223000	Flanking Active TSS	HMEC	breast
43	chr11:65222200-65223200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr11:65222200-65223200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr11:65222200-65223200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr11:65222200-65223200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:65222200-65223200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:65222200-65223200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr11:65222200-65223200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr11:65222200-65223200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links