Variant report

Variant	rs12288911
Chromosome Location	chr11:65684271-65684272
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	chr11:65682505-65685837	HCT-116	colon:	n/a	n/a
2	POLR2A	chr11:65682313-65684298	SK-N-SH	brain:	n/a	n/a
3	MAZ	chr11:65684129-65687972	IMR90	lung:	n/a	chr11:65687019-65687026 chr11:65687018-65687027 chr11:65687018-65687028 chr11:65687016-65687029 chr11:65687017-65687028 chr11:65687367-65687377 chr11:65687018-65687027 chr11:65687017-65687028 chr11:65687017-65687027 chr11:65687354-65687363 chr11:65687122-65687132 chr11:65687017-65687028
4	POLR2A	chr11:65681960-65688394	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr11:65683488-65684280	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:65682124-65685845	K562	blood:	n/a	n/a
7	POLR2A	chr11:65682051-65685006	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr11:65683247-65684328	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr11:65682189-65684526	HL-60	blood:	n/a	n/a
10	POLR2A	chr11:65681389-65688769	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr11:65682362-65684676	GM12892	blood:	n/a	n/a
12	POLR2A	chr11:65682430-65684736	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr11:65682380-65686585	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:65683741-65684518	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:65683005-65684990	K562	blood:	n/a	n/a
16	POLR2A	chr11:65682054-65686599	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:65682270-65687707	K562	blood:	n/a	n/a
18	POLR2A	chr11:65682661-65686627	HCT-116	colon:	n/a	n/a
19	POLR2A	chr11:65681773-65687130	U87	brain:	n/a	n/a
20	POLR2A	chr11:65683210-65684327	PFSK-1	brain:	n/a	n/a
21	FOS	chr11:65684142-65684342	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr11:65684181-65684567	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr11:65684207-65684468	HepG2	liver:	n/a	n/a
24	MAX	chr11:65682036-65684689	A549	lung:	n/a	chr11:65683301-65683310
25	POLR2A	chr11:65682254-65684912	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr11:65684084-65684827	K562	blood:	n/a	n/a
27	POLR2A	chr11:65684259-65684330	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr11:65682898-65684589	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr11:65677999-65686383	U87	brain:	n/a	n/a
30	POLR2A	chr11:65684258-65684839	GM12892	blood:	n/a	n/a
31	TCF7L2	chr11:65684122-65684381	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr11:65678005-65686377	U87	brain:	n/a	n/a
33	POLR2A	chr11:65682095-65686648	GM12892	blood:	n/a	n/a
34	POLR2A	chr11:65682320-65687300	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr11:65682128-65684360	ProgFib	skin:	n/a	n/a
36	POLR2A	chr11:65682548-65686605	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:65684195-65684638	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65485702..65488169-chr11:65683105..65685418,2	MCF-7	breast:
2	chr11:65683165..65691632-chr11:65723620..65730701,28	MCF-7	breast:
3	chr11:65485621..65487776-chr11:65682434..65684591,2	K562	blood:
4	chr11:65684149..65688321-chr11:65727274..65731998,8	MCF-7	breast:
5	chr11:65682614..65684925-chr11:65768572..65770745,2	MCF-7	breast:
6	chr11:65683260..65685556-chr11:65700127..65702595,2	MCF-7	breast:
7	chr11:65624095..65629782-chr11:65682347..65689302,13	MCF-7	breast:
8	chr11:65652289..65653954-chr11:65682790..65684539,2	MCF-7	breast:
9	chr11:65650579..65663306-chr11:65677153..65690311,39	MCF-7	breast:
10	chr11:65684023..65687163-chr11:65778751..65782457,4	MCF-7	breast:
11	chr11:65622510..65630779-chr11:65675126..65689187,23	MCF-7	breast:

Variant related genes	Relation type
DRAP1	TF binding region
ENSG00000175602	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10791832	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10896065	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs11227337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227338	1.00[EUR][1000 genomes]
rs11227341	1.00[AMR][1000 genomes]
rs11825885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12289280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575085	1.00[TSI][hapmap]
rs653955	1.00[CEU][hapmap]
rs7940700	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7941052	1.00[EUR][1000 genomes]
rs9326360	1.00[CEU][hapmap]
rs9326361	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9795434	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs9919533	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers 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 target site	178 gene(s)	inside rSNPs	diseases
4	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers 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 target site	178 gene(s)	inside rSNPs	diseases
5	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
6	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
10	nsv897767	chr11:65683531-65690206	Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12288911	RHOXF2	trans	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65679400-65685200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:65679600-65684400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:65679600-65684400	Enhancers	Placenta	Placenta
4	chr11:65680000-65684400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:65680000-65684600	Weak transcription	Fetal Lung	lung
6	chr11:65681600-65685400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:65681800-65684800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:65682000-65684800	Enhancers	Esophagus	oesophagus
9	chr11:65682000-65685200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:65682000-65685400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr11:65682200-65684400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:65682200-65684400	Enhancers	Primary B cells from peripheral blood	blood
13	chr11:65682200-65684400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:65682200-65684800	Enhancers	Ovary	ovary
15	chr11:65682200-65684800	Enhancers	Psoas Muscle	Psoas
16	chr11:65682200-65684800	Enhancers	Right Ventricle	heart
17	chr11:65682200-65685000	Genic enhancers	Fetal Stomach	stomach
18	chr11:65682200-65685000	Enhancers	Pancreas	Pancrea
19	chr11:65682200-65685200	Enhancers	Left Ventricle	heart
20	chr11:65682200-65685800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:65682400-65684400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:65682400-65684400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:65682400-65684400	Enhancers	Spleen	Spleen
24	chr11:65682400-65684600	Enhancers	Lung	lung
25	chr11:65682400-65684800	Enhancers	Duodenum Mucosa	Duodenum
26	chr11:65682400-65685200	Enhancers	Brain Cingulate Gyrus	brain
27	chr11:65682400-65685200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr11:65682600-65684400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr11:65682600-65684400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr11:65682600-65684800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:65682600-65685000	Enhancers	Brain Hippocampus Middle	brain
32	chr11:65682600-65685400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:65682600-65685400	Enhancers	Brain Angular Gyrus	brain
34	chr11:65682600-65685400	Enhancers	Brain Substantia Nigra	brain
35	chr11:65682600-65685600	Enhancers	Fetal Heart	heart
36	chr11:65682600-65686000	Flanking Active TSS	Hela-S3	cervix
37	chr11:65682600-65686400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:65682800-65684400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr11:65682800-65684800	Enhancers	Brain Anterior Caudate	brain
40	chr11:65682800-65684800	Flanking Active TSS	A549	lung
41	chr11:65682800-65685200	Enhancers	Small Intestine	intestine
42	chr11:65682800-65685400	Enhancers	Primary B cells from cord blood	blood
43	chr11:65682800-65685400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr11:65682800-65686200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:65682800-65686200	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr11:65683000-65684400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr11:65683000-65684400	Weak transcription	Liver	Liver
48	chr11:65683000-65684600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr11:65683200-65684400	Weak transcription	Gastric	stomach
50	chr11:65683200-65684400	Weak transcription	Rectal Mucosa Donor 31	rectum

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