Variant report

Variant	rs1194076
Chromosome Location	chr11:65336544-65336545
allele	A/C
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	POLR2A	chr11:65336533-65338314	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:65336528-65338307	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr11:65336527-65338249	GM12878	blood:	n/a	n/a
4	HCFC1	chr11:65335547-65338561	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr11:65336337-65338250	A549	lung:	n/a	chr11:65337902-65337915 chr11:65336529-65336537
6	POLR2A	chr11:65336472-65338317	HepG2	liver:	n/a	n/a
7	MXI1	chr11:65336214-65338802	SK-N-SH	brain:	n/a	chr11:65337705-65337720
8	MAZ	chr11:65336306-65338566	IMR90	lung:	n/a	n/a
9	NRF1	chr11:65336494-65338145	SK-N-SH	brain:	n/a	chr11:65337501-65337512 chr11:65337501-65337515 chr11:65337498-65337512 chr11:65337259-65337273 chr11:65337501-65337512 chr11:65337566-65337575 chr11:65337503-65337512
10	JUN	chr11:65336260-65338579	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65336349..65338989-chr11:65428353..65432348,4	MCF-7	breast:
2	chr11:65182317..65198249-chr11:65333937..65346467,45	MCF-7	breast:
3	chr11:65335401..65344755-chr11:65379602..65385163,20	K562	blood:
4	chr11:65262109..65269742-chr11:65336183..65344125,16	MCF-7	breast:
5	chr11:65263786..65274103-chr11:65335962..65346813,28	MCF-7	breast:
6	chr11:65336222..65339291-chr11:65623626..65626992,4	K562	blood:
7	chr11:65335492..65337071-chr17:7737574..7739676,2	MCF-7	breast:
8	chr11:65336061..65346997-chr11:65371025..65390625,42	MCF-7	breast:
9	chr11:65336026..65338505-chr11:65655594..65658699,3	MCF-7	breast:
10	chr11:65264659..65267625-chr11:65336211..65338117,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTBP3-1	chr11:65335953-65337894	ENSG00000260233.1
2	lnc-LTBP3-1	chr11:65333533-65337942	NONHSAT022168

Variant related genes	Relation type
SSSCA1	TF binding region
FAM89B	TF binding region
ENSG00000197136	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10896009	0.82[MEX][hapmap]
rs10896012	0.83[JPT][hapmap];0.82[MEX][hapmap]
rs10896015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896016	0.80[JPT][hapmap]
rs11227221	0.80[JPT][hapmap]
rs1151496	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151517	0.80[JPT][hapmap]
rs1152619	0.88[TSI][hapmap]
rs1152620	0.83[CEU][hapmap];0.94[TSI][hapmap]
rs11601767	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs1194077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194104	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270054	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12360896	0.82[MEX][hapmap]
rs1346	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs17146964	0.82[MEX][hapmap]
rs1783541	0.83[JPT][hapmap]
rs1787663	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs2510078	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3200401	0.83[JPT][hapmap];0.82[MEX][hapmap]
rs3782091	0.80[JPT][hapmap]
rs4244811	0.80[JPT][hapmap]
rs600231	0.84[TSI][hapmap]
rs67924081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947791	0.83[JPT][hapmap];0.82[MEX][hapmap]

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	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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
16	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
17	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active 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	78 gene(s)	inside rSNPs	diseases
18	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
19	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
20	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
21	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
22	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
23	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' 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	227 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1194076	NEAT1	cis	Nerve Tibial	GTEx
rs1194076	CDK2AP2	cis	cerebellum	SCAN
rs1194076	SCGB2A1	cis	cerebellum	SCAN
rs1194076	BBS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65326800-65336800	Weak transcription	Aorta	Aorta
2	chr11:65329000-65336800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:65329400-65336600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:65331800-65336600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:65333400-65336600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:65334400-65336600	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr11:65334400-65336600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr11:65335400-65336600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:65335400-65336600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:65335400-65336600	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr11:65335600-65336600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr11:65335600-65336600	Enhancers	Fetal Intestine Large	intestine
13	chr11:65335800-65336800	Enhancers	Stomach Mucosa	stomach
14	chr11:65336000-65336600	Enhancers	Placenta	Placenta
15	chr11:65336000-65336600	Enhancers	Fetal Thymus	thymus
16	chr11:65336000-65336600	Enhancers	Spleen	Spleen
17	chr11:65336200-65336600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr11:65336200-65336600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:65336200-65336600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
20	chr11:65336200-65336600	Genic enhancers	Fetal Muscle Leg	muscle
21	chr11:65336200-65336600	Genic enhancers	Fetal Stomach	stomach
22	chr11:65336200-65336600	Genic enhancers	Right Atrium	heart
23	chr11:65336200-65336600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr11:65336200-65336600	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr11:65336200-65336600	Enhancers	NH-A	brain
26	chr11:65336200-65336800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:65336200-65336800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr11:65336200-65336800	Enhancers	Psoas Muscle	Psoas
29	chr11:65336200-65336800	Flanking Active TSS	GM12878-XiMat	blood
30	chr11:65336200-65336800	Enhancers	HUVEC	blood vessel
31	chr11:65336200-65337000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:65336200-65337000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:65336200-65337000	Flanking Active TSS	NHLF	lung
34	chr11:65336200-65337200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr11:65336200-65337200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr11:65336200-65337200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:65336200-65337200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr11:65336200-65337200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:65336200-65337200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:65336200-65337200	Flanking Active TSS	Hela-S3	cervix
41	chr11:65336200-65337400	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr11:65336200-65337400	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr11:65336200-65337400	Flanking Active TSS	Fetal Brain Male	brain
44	chr11:65336200-65337400	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr11:65336200-65337400	Flanking Active TSS	HMEC	breast
46	chr11:65336200-65337400	Flanking Active TSS	K562	blood
47	chr11:65336200-65337600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr11:65336200-65337600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:65336200-65337600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr11:65336200-65337600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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