Variant report

Variant	rs613316
Chromosome Location	chr11:65195255-65195256
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:94)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:94 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr11:10830163..10830709-chr11:65194943..65195510,2	Hela-S3	cervix:
2	chr1:145447323..145449009-chr11:65194449..65196745,2	K562	blood:
3	chr11:65194969..65195924-chr14:75745666..75746339,2	Hela-S3	cervix:
4	chr11:65047579..65049698-chr11:65194301..65197183,2	K562	blood:
5	chr11:65193125..65195904-chr6:26019667..26021625,2	K562	blood:
6	chr11:65193834..65196354-chr2:47401759..47403900,2	MCF-7	breast:
7	chr11:65189010..65195293-chr11:65321323..65327708,15	K562	blood:
8	chr11:65194680..65197521-chr11:65429706..65431467,2	MCF-7	breast:
9	chr1:247094751..247095451-chr11:65195252..65195789,2	Hela-S3	cervix:
10	chr11:65193966..65195508-chr11:65340002..65341813,2	K562	blood:
11	chr11:65096021..65098994-chr11:65192739..65196901,5	K562	blood:
12	chr11:65096021..65098876-chr11:65192739..65195995,3	K562	blood:
13	chr11:64895813..64897424-chr11:65195099..65197193,2	MCF-7	breast:
14	chr1:11966803..11968507-chr11:65194382..65198671,3	K562	blood:
15	chr11:65194558..65195488-chr18:11979959..11980471,2	Hela-S3	cervix:
16	chr1:43147867..43150199-chr11:65194283..65195810,2	K562	blood:
17	chr11:64878111..64880272-chr11:65194230..65195799,2	MCF-7	breast:
18	chr11:65194433..65196288-chr7:5632160..5635076,2	K562	blood:
19	chr11:65195138..65195969-chr2:47403254..47404091,2	Hela-S3	cervix:
20	chr1:43147649..43150199-chr11:65194283..65196724,3	K562	blood:
21	chr11:65195152..65197902-chr11:65335225..65338216,2	K562	blood:
22	chr11:65192842..65197506-chr11:65307614..65311008,4	K562	blood:
23	chr11:65194845..65195564-chr6:32939218..32940198,2	Hela-S3	cervix:
24	chr11:65194383..65196856-chr8:101964338..101966893,2	MCF-7	breast:
25	chr11:65194758..65195409-chr15:91475309..91475885,2	Hela-S3	cervix:
26	chr11:65194190..65196733-chr5:130499306..130502020,2	MCF-7	breast:
27	chr11:65193954..65196050-chr19:13264142..13265922,2	K562	blood:
28	chr11:65194565..65197365-chr6:26123197..26126081,2	K562	blood:
29	chr11:65195103..65195676-chr5:40679427..40679946,2	Hela-S3	cervix:
30	chr1:149223128..149224739-chr11:65193502..65196439,3	K562	blood:
31	chr11:63712054..63714315-chr11:65194541..65196284,2	K562	blood:
32	chr11:65194133..65196773-chr16:70728279..70731009,2	K562	blood:
33	chr11:65194263..65195445-chr17:57915506..57916561,3	Hela-S3	cervix:
34	chr11:65193714..65195706-chr3:171078041..171079983,2	MCF-7	breast:
35	chr11:65195117..65198166-chr16:67901081..67904062,3	MCF-7	breast:
36	chr11:65195036..65198002-chr3:176913257..176915574,2	MCF-7	breast:
37	chr11:65195093..65195733-chr8:134303847..134304392,2	Hela-S3	cervix:
38	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
39	chr11:64971229..64973942-chr11:65195217..65197013,2	K562	blood:
40	chr11:65193724..65196032-chr17:79823722..79825538,2	K562	blood:
41	chr11:65081479..65084201-chr11:65193891..65195516,2	MCF-7	breast:
42	chr1:1538541..1540935-chr11:65194379..65196636,2	K562	blood:
43	chr11:65195008..65195880-chr13:111367164..111367961,2	Hela-S3	cervix:
44	chr1:38470594..38472979-chr11:65194613..65196590,2	K562	blood:
45	chr11:65194654..65195277-chr14:24711490..24711994,2	Hela-S3	cervix:
46	chr11:65193612..65196519-chr5:68460804..68462956,2	MCF-7	breast:
47	chr1:146555650..146556332-chr11:65194563..65195527,2	Hela-S3	cervix:
48	chr11:65193019..65196313-chr6:26214242..26217994,3	K562	blood:
49	chr11:65193729..65195292-chr11:65318361..65320599,2	MCF-7	breast:
50	chr11:65193280..65195558-chr6:27102122..27104681,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTBP3-2	chr11:65193086-65204597	NONHSAT022110

No data

Variant related genes	Relation type
ENSG00000117143	Chromatin interaction
ENSG00000177565	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000122565	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000102898	Chromatin interaction
ENSG00000259788	Chromatin interaction
ENSG00000107821	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000173727	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000184508	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000171604	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000169567	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000127588	Chromatin interaction
ENSG00000116514	Chromatin interaction
ENSG00000103043	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000188486	Chromatin interaction
ENSG00000075618	Chromatin interaction
ENSG00000250635	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000183386	Chromatin interaction
ENSG00000065978	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000229848	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000267598	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000147050	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000153207	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000270526	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000257453	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000200087	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000116266	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000134470	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000171522	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000229947	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs512715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580933	0.81[JPT][hapmap]
rs595366	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs673753	0.81[JPT][hapmap]
rs674485	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694243	0.80[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs613316	NEAT1	cis	Thyroid	GTEx
rs613316	NEAT1	cis	lung	GTEx
rs613316	NEAT1	cis	Muscle Skeletal	GTEx
rs613316	NEAT1	cis	Esophagus Muscularis	GTEx
rs613316	LOC728975	cis	brain	BrainEAC
rs613316	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs613316	NEAT1	cis	Nerve Tibial	GTEx
rs613316	NEAT1	cis	Artery Tibial	GTEx
rs613316	NEAT1	cis	Esophagus Mucosa	GTEx
rs613316	NEAT1	cis	Adipose Subcutaneous	GTEx
rs613316	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65186200-65197400	Active TSS	Psoas Muscle	Psoas
2	chr11:65189400-65195600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:65189400-65195800	Active TSS	Ovary	ovary
4	chr11:65190400-65195600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
5	chr11:65190400-65195800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
6	chr11:65190400-65196000	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr11:65190400-65196200	Transcr. at gene 5' and 3'	NHLF	lung
8	chr11:65190400-65196800	Transcr. at gene 5' and 3'	K562	blood
9	chr11:65190400-65199800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:65190400-65200400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
11	chr11:65190600-65206600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:65190800-65196000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
13	chr11:65190800-65196200	Transcr. at gene 5' and 3'	A549	lung
14	chr11:65190800-65196400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:65190800-65201000	Transcr. at gene 5' and 3'	Osteobl	bone
16	chr11:65191000-65196000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:65191000-65197800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:65191000-65206800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:65191200-65195400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:65191200-65198000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
21	chr11:65191400-65196200	Transcr. at gene 5' and 3'	Left Ventricle	heart
22	chr11:65191400-65196400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
23	chr11:65191400-65198200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:65191600-65197000	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
25	chr11:65191800-65195400	Transcr. at gene 5' and 3'	Placenta	Placenta
26	chr11:65191800-65196000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:65191800-65196200	Transcr. at gene 5' and 3'	HSMM	muscle
28	chr11:65192800-65195800	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:65192800-65196200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
30	chr11:65192800-65200600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:65193000-65196200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:65193000-65198600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr11:65193200-65196200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr11:65193200-65198000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr11:65193800-65195600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
36	chr11:65193800-65195600	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
37	chr11:65193800-65196000	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
38	chr11:65193800-65196200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:65193800-65209800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr11:65194000-65195600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:65194000-65195600	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
42	chr11:65194000-65195600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
43	chr11:65194000-65195800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:65194000-65196200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr11:65194000-65196200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr11:65194000-65196200	Transcr. at gene 5' and 3'	Lung	lung
47	chr11:65194000-65197000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
48	chr11:65194000-65198200	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr11:65194000-65198200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr11:65194000-65198600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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