Variant report

Variant	rs12224858
Chromosome Location	chr11:65327655-65327656
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	FOSL2	chr11:65327401-65327946	MCF-7	breast:	n/a	chr11:65327674-65327685
2	POLR2A	chr11:65327420-65327707	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr11:65327095-65327860	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr11:65327379-65328538	A549	lung:	n/a	n/a
5	USF2	chr11:65327485-65327825	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr11:65325547-65328080	ECC-1	luminal epithelium:	n/a	chr11:65326414-65326424
7	JUN	chr11:65327123-65328509	K562	blood:	n/a	n/a
8	FOSL2	chr11:65326211-65328491	A549	lung:	n/a	chr11:65326808-65326816 chr11:65327674-65327685 chr11:65326806-65326818
9	RFX5	chr11:65327602-65327975	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:65327497-65328104	HepG2	liver:	n/a	n/a
11	FOSL2	chr11:65327311-65328512	A549	lung:	n/a	chr11:65327674-65327685
12	FOSL2	chr11:65327413-65327896	HepG2	liver:	n/a	chr11:65327674-65327685
13	JUND	chr11:65327508-65328243	Hela-S3	cervix:	n/a	chr11:65327675-65327686
14	JUND	chr11:65327521-65327795	H1-hESC	embryonic stem cell:	n/a	chr11:65327675-65327686
15	JUND	chr11:65327545-65327778	HepG2	liver:	n/a	chr11:65327675-65327686
16	RXRA	chr11:65327400-65328832	SK-N-SH	brain:	n/a	n/a
17	GTF2F1	chr11:65327429-65327884	Hela-S3	cervix:	n/a	n/a
18	FOS	chr11:65327253-65328158	MCF10A-Er-Src	breast:	n/a	chr11:65328108-65328119
19	FOS	chr11:65327443-65328362	HUVEC	blood vessel:	n/a	chr11:65328108-65328119
20	ZBTB7A	chr11:65325554-65328426	ECC-1	luminal epithelium:	n/a	chr11:65325577-65325585 chr11:65327180-65327191
21	POLR2A	chr11:65327449-65327997	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr11:65326451-65328572	U87	brain:	n/a	n/a
23	NR3C1	chr11:65327459-65328312	A549	lung:	n/a	chr11:65327732-65327745
24	POLR2A	chr11:65325540-65328890	U87	brain:	n/a	n/a
25	FOSL2	chr11:65327459-65328268	SK-N-SH	brain:	n/a	chr11:65327674-65327685
26	FOS	chr11:65327209-65327871	MCF10A-Er-Src	breast:	n/a	n/a
27	RXRA	chr11:65327466-65328608	SK-N-SH	brain:	n/a	n/a
28	FOSL2	chr11:65325586-65328762	SK-N-SH	brain:	n/a	chr11:65326109-65326118 chr11:65326808-65326816 chr11:65327674-65327685 chr11:65326806-65326818 chr11:65326114-65326123
29	REST	chr11:65327241-65328526	A549	lung:	n/a	chr11:65327276-65327289
30	FOS	chr11:65327512-65327850	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr11:65327128-65328792	HUVEC	blood vessel:	n/a	n/a
32	EP300	chr11:65325583-65328254	ECC-1	luminal epithelium:	n/a	chr11:65325849-65325865 chr11:65326384-65326398 chr11:65326643-65326659 chr11:65326362-65326371 chr11:65325862-65325878 chr11:65325863-65325872 chr11:65326040-65326056 chr11:65325853-65325869 chr11:65326647-65326663
33	MAX	chr11:65327611-65327908	Hela-S3	cervix:	n/a	chr11:65327802-65327812
34	EP300	chr11:65327384-65328067	ECC-1	luminal epithelium:	n/a	n/a
35	FOSL1	chr11:65325829-65328395	HCT-116	colon:	n/a	chr11:65326109-65326118 chr11:65326808-65326816 chr11:65326806-65326818 chr11:65326114-65326123
36	NFIC	chr11:65325551-65328314	ECC-1	luminal epithelium:	n/a	n/a
37	TCF12	chr11:65327401-65327911	A549	lung:	n/a	n/a
38	YY1	chr11:65327448-65327905	HCT-116	colon:	n/a	n/a
39	POLR2A	chr11:65327487-65327796	A549	lung:	n/a	n/a
40	ELF1	chr11:65327383-65327928	A549	lung:	n/a	n/a
41	TCF12	chr11:65325604-65328212	ECC-1	luminal epithelium:	n/a	chr11:65326414-65326424
42	FOSL1	chr11:65326492-65328448	HCT-116	colon:	n/a	chr11:65326808-65326816 chr11:65326806-65326818
43	EP300	chr11:65327334-65328377	A549	lung:	n/a	n/a
44	BCL3	chr11:65327421-65328806	A549	lung:	n/a	n/a
45	JUND	chr11:65327546-65327836	HepG2	liver:	n/a	chr11:65327675-65327686
46	CREB1	chr11:65327497-65327945	A549	lung:	n/a	n/a
47	TEAD4	chr11:65327420-65328275	ECC-1	luminal epithelium:	n/a	n/a
48	KAP1	chr11:65327539-65327992	U2OS	brain:	n/a	n/a
49	NR3C1	chr11:65327570-65327894	A549	lung:	n/a	chr11:65327732-65327745
50	MAX	chr11:65325449-65328939	A549	lung:	n/a	chr11:65326583-65326593 chr11:65327802-65327812 chr11:65325980-65325990

No.	Distal block	Cell Line	Cell type
1	chr11:65188903..65194388-chr11:65323256..65328284,10	MCF-7	breast:
2	chr11:65189010..65195293-chr11:65321323..65327708,15	K562	blood:
3	chr11:65188846..65191466-chr11:65325823..65328502,2	MCF-7	breast:
4	chr11:65264952..65268870-chr11:65322730..65327860,7	K562	blood:
5	chr11:65326472..65327992-chr11:65379929..65382834,2	MCF-7	breast:
6	chr11:65264479..65268560-chr11:65318003..65330456,22	MCF-7	breast:
7	chr11:65184371..65196984-chr11:65316952..65328208,29	K562	blood:

Variant related genes	Relation type
LTBP3	TF binding region
ENSG00000173327	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10896017	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227223	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227227	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236684	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4099470	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
16	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
17	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
18	nsv897730	chr11:65302893-65376484	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12224858	NEAT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65325800-65328800	Enhancers	Fetal Brain Male	brain
2	chr11:65326000-65330000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:65326200-65328200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr11:65326200-65328800	Enhancers	Fetal Heart	heart
5	chr11:65326200-65328800	Flanking Active TSS	A549	lung
6	chr11:65326200-65329000	Enhancers	NHDF-Ad	bronchial
7	chr11:65326400-65327800	Enhancers	HMEC	breast
8	chr11:65326400-65328000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr11:65326400-65328000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:65326400-65328200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr11:65326400-65328200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:65326400-65328200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr11:65326400-65328400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:65326400-65328400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr11:65326400-65328600	Enhancers	Gastric	stomach
16	chr11:65326400-65328800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:65326400-65328800	Enhancers	Brain Angular Gyrus	brain
18	chr11:65326400-65328800	Enhancers	Esophagus	oesophagus
19	chr11:65326400-65328800	Enhancers	Left Ventricle	heart
20	chr11:65326400-65328800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr11:65326400-65328800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr11:65326400-65328800	Enhancers	Stomach Mucosa	stomach
23	chr11:65326400-65328800	Flanking Active TSS	HepG2	liver
24	chr11:65326400-65329000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:65326400-65329000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:65326400-65329000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:65326400-65329000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:65326400-65329000	Enhancers	Liver	Liver
29	chr11:65326400-65329000	Enhancers	Lung	lung
30	chr11:65326400-65329000	Enhancers	Ovary	ovary
31	chr11:65326400-65329000	Enhancers	NHLF	lung
32	chr11:65326400-65329200	Enhancers	Placenta	Placenta
33	chr11:65326400-65329400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:65326400-65329600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:65326400-65329800	Enhancers	HUVEC	blood vessel
36	chr11:65326600-65327800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr11:65326600-65327800	Weak transcription	Psoas Muscle	Psoas
38	chr11:65326600-65328400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
39	chr11:65326600-65328400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
40	chr11:65326600-65328400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:65326600-65328400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:65326600-65328400	Enhancers	Pancreas	Pancrea
43	chr11:65326600-65328600	Enhancers	Adipose Nuclei	Adipose
44	chr11:65326600-65328600	Enhancers	Right Ventricle	heart
45	chr11:65326600-65328800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
46	chr11:65326600-65328800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:65326600-65328800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr11:65326600-65328800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr11:65326600-65328800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:65326600-65328800	Enhancers	Brain Inferior Temporal Lobe	brain

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