Variant report

Variant	rs1616810
Chromosome Location	chr11:65220105-65220106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:65220089-65220236	Hela-S3	cervix:	n/a	chr11:65220109-65220120
2	POLR2A	chr11:65219749-65221240	U87	brain:	n/a	n/a
3	POLR2A	chr11:65220010-65221032	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr11:65220098-65220215	A549	lung:	n/a	chr11:65220109-65220120
5	TCF12	chr11:65219871-65221149	SK-N-SH	brain:	n/a	chr11:65220699-65220709
6	NFIC	chr11:65220066-65221003	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr11:65220036-65221065	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr11:65219915-65221094	SK-N-SH	brain:	n/a	chr11:65220699-65220709
9	EP300	chr11:65220097-65220659	SK-N-SH_RA	brain:	n/a	chr11:65220502-65220509
10	POLR2A	chr11:65219867-65221167	U87	brain:	n/a	n/a
11	POLR2A	chr11:65219846-65221167	U87	brain:	n/a	n/a
12	CEBPB	chr11:65220045-65220245	HepG2	liver:	n/a	chr11:65220109-65220120
13	POLR2A	chr11:65219993-65220851	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr11:65220101-65220783	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr11:65219800-65221139	U87	brain:	n/a	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP000769.1-1	chr11:65219924-65221119	NONHSAT022120

Variant related genes	Relation type
ENSG00000173727	TF binding region
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10896001	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11227204	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11822111	0.82[AMR][1000 genomes]
rs1621277	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1626021	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1784100	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1784101	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1784858	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784859	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1784860	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2105608	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508711	0.81[ASN][1000 genomes]
rs2508712	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2846861	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957268	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957269	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3015965	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015966	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3016343	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132743	0.81[EUR][1000 genomes]
rs3132767	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs587080	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs587390	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs588298	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs602838	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604676	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs605035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs660588	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs661403	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682845	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7114809	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7934628	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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
22	esv32703	chr11:65213860-65222026	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	esv3422413	chr11:65217601-65220149	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1616810	NEAT1	cis	Nerve Tibial	GTEx
rs1616810	NEAT1	cis	Esophagus Muscularis	GTEx
rs1616810	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs1616810	NEAT1	cis	Muscle Skeletal	GTEx
rs1616810	NEAT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65206600-65222000	Weak transcription	Fetal Kidney	kidney
2	chr11:65210000-65222000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:65210000-65222200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:65210800-65222000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:65211400-65222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:65211600-65221800	Weak transcription	HUVEC	blood vessel
7	chr11:65212200-65221800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:65212200-65222000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:65212200-65222200	Weak transcription	Liver	Liver
10	chr11:65212400-65222000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr11:65212400-65222000	Weak transcription	Aorta	Aorta
12	chr11:65212400-65222000	Weak transcription	Fetal Lung	lung
13	chr11:65212600-65222000	Weak transcription	Brain Anterior Caudate	brain
14	chr11:65212800-65221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:65212800-65222000	Weak transcription	Primary T cells from cord blood	blood
16	chr11:65212800-65222000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:65212800-65222200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:65212800-65222400	Weak transcription	Stomach Mucosa	stomach
19	chr11:65213000-65221800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:65213000-65222000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:65213200-65221800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:65213400-65220200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:65213400-65222000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:65213400-65222000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:65213800-65222000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:65213800-65222200	Weak transcription	Gastric	stomach
27	chr11:65213800-65222200	Weak transcription	Pancreas	Pancrea
28	chr11:65214000-65220200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:65214000-65221800	Weak transcription	Right Atrium	heart
30	chr11:65214200-65220200	Weak transcription	NH-A	brain
31	chr11:65214200-65220400	Weak transcription	Lung	lung
32	chr11:65214200-65222000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:65214200-65222000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:65214200-65222200	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:65214400-65220200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:65214400-65221800	Weak transcription	Thymus	Thymus
37	chr11:65214400-65221800	Weak transcription	Spleen	Spleen
38	chr11:65214400-65222000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:65214400-65222200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:65214400-65222200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:65214600-65220200	Weak transcription	Esophagus	oesophagus
42	chr11:65214600-65220200	Weak transcription	Left Ventricle	heart
43	chr11:65214600-65220200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:65214600-65220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:65214600-65221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:65214600-65221400	Weak transcription	Colonic Mucosa	Colon
47	chr11:65214600-65221400	Weak transcription	Right Ventricle	heart
48	chr11:65214600-65221800	Weak transcription	Ovary	ovary
49	chr11:65214600-65222000	Weak transcription	Brain Substantia Nigra	brain
50	chr11:65214600-65222000	Weak transcription	Rectal Mucosa Donor 29	rectum

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