Variant report

Variant	rs508286
Chromosome Location	chr11:65208118-65208119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65204713-65209032	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr11:65183014-65218224	IMR90	lung:	n/a	chr11:65189696-65189706 chr11:65213009-65213016
3	POLR2A	chr11:65204887-65208966	A549	lung:	n/a	n/a
4	POLR2A	chr11:65188590-65214677	MCF-7	breast:	n/a	n/a
5	SPI1	chr11:65208028-65208793	GM12878	blood:	n/a	n/a
6	RUNX3	chr11:65207847-65208935	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:65188505-65217165	ProgFib	skin:	n/a	n/a
8	MBD4	chr11:65207710-65208137	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:65204788-65208894	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr11:65207790-65208272	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:65207684-65208152	HL-60	blood:	n/a	n/a
12	POLR2A	chr11:65208017-65208869	GM12878	blood:	n/a	n/a
13	MTA3	chr11:65208107-65209081	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:65204679-65217682	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr11:65204683-65208176	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr11:65190093-65217195	HepG2	liver:	n/a	n/a
17	POLR2A	chr11:65208007-65208156	K562	blood:	n/a	n/a
18	POLR2A	chr11:65207693-65208127	K562	blood:	n/a	n/a
19	POLR2A	chr11:65207657-65208119	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:65206963-65208960	HepG2	liver:	n/a	n/a
21	RUNX3	chr11:65207710-65208125	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:65206935-65217365	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:65204686-65217768	U87	brain:	n/a	n/a
24	POLR2A	chr11:65207005-65208122	GM12878	blood:	n/a	n/a
25	NFATC1	chr11:65207485-65208169	GM12878	blood:	n/a	n/a
26	STAT5A	chr11:65207425-65208140	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:65207571-65209015	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr11:65189948-65210218	U87	brain:	n/a	n/a
29	POLR2A	chr11:65204710-65210230	HepG2	liver:	n/a	n/a
30	POLR2A	chr11:65204795-65208964	IMR90	lung:	n/a	n/a
31	FOXM1	chr11:65207998-65209135	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:65189948-65217642	U87	brain:	n/a	n/a
33	POLR2A	chr11:65204692-65218221	U87	brain:	n/a	n/a
34	POLR2A	chr11:65207668-65209012	K562	blood:	n/a	n/a
35	POLR2A	chr11:65204793-65208915	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr11:65188357-65217120	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr11:65190096-65215252	K562	blood:	n/a	n/a
38	POLR2A	chr11:65207670-65208923	K562	blood:	n/a	n/a
39	POLR2A	chr11:65207152-65217137	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr11:65204649-65208973	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:

No data

Variant related genes	Relation type
NEAT1	TF binding region
ENSG00000173727	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000270526	Chromatin interaction

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

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

rs_ID	r²[population]
rs11602839	0.85[EUR][1000 genomes]
rs2073801	0.85[EUR][1000 genomes]
rs2904976	0.85[EUR][1000 genomes]
rs475967	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs481335	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs550015	0.85[EUR][1000 genomes]
rs550894	0.91[EUR][1000 genomes]
rs580933	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61154080	0.83[EUR][1000 genomes]
rs666834	0.85[EUR][1000 genomes]
rs673753	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs508286	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65193800-65209800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65197800-65209200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:65198000-65209400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr11:65198000-65216000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:65198200-65209400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:65198800-65209400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:65200600-65211600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
8	chr11:65200600-65214200	Strong transcription	NH-A	brain
9	chr11:65201400-65209200	Strong transcription	Fetal Muscle Leg	muscle
10	chr11:65201600-65208200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:65201600-65211600	Genic enhancers	Brain Substantia Nigra	brain
12	chr11:65201800-65208400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:65202200-65208400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:65202600-65214400	Genic enhancers	A549	lung
15	chr11:65203200-65211600	Strong transcription	HUVEC	blood vessel
16	chr11:65203400-65212200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:65204200-65209200	Weak transcription	Pancreas	Pancrea
18	chr11:65204400-65210600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
19	chr11:65205200-65214400	Genic enhancers	Placenta	Placenta
20	chr11:65205400-65210600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:65205400-65211600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:65205400-65212400	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr11:65205600-65208400	Strong transcription	HSMM	muscle
24	chr11:65205600-65209200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:65205600-65209400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:65205600-65209400	Weak transcription	Gastric	stomach
27	chr11:65205600-65209600	Weak transcription	Small Intestine	intestine
28	chr11:65205600-65209800	Weak transcription	Dnd41	blood
29	chr11:65205600-65214800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:65205600-65217600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:65205800-65208400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:65205800-65209400	Weak transcription	Esophagus	oesophagus
33	chr11:65205800-65209400	Strong transcription	Lung	lung
34	chr11:65205800-65209400	Weak transcription	Thymus	Thymus
35	chr11:65205800-65209800	Weak transcription	Psoas Muscle	Psoas
36	chr11:65205800-65211000	Weak transcription	Aorta	Aorta
37	chr11:65206000-65208400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr11:65206200-65208400	Weak transcription	Fetal Heart	heart
39	chr11:65206200-65209400	Weak transcription	Ovary	ovary
40	chr11:65206200-65211200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:65206200-65211200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr11:65206200-65212400	Genic enhancers	Duodenum Mucosa	Duodenum
43	chr11:65206400-65208600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:65206400-65208600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:65206400-65209000	Enhancers	Brain Anterior Caudate	brain
46	chr11:65206400-65210800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr11:65206400-65210800	Weak transcription	Stomach Mucosa	stomach
48	chr11:65206400-65213000	Genic enhancers	Osteobl	bone
49	chr11:65206600-65208600	Enhancers	HepG2	liver
50	chr11:65206600-65209200	Enhancers	Primary T helper cells fromperipheralblood	blood

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