Variant report

Variant	rs1491944
Chromosome Location	chr12:40619681-40619682
allele	C/T
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	chr12:40619298-40619782	A549	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
2	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
3	KAP1	chr12:40618416-40619717	HEK293	kidney:	n/a	n/a
4	RCOR1	chr12:40619571-40620834	GM12878	blood:	n/a	n/a
5	CEBPB	chr12:40619462-40619788	H1-hESC	embryonic stem cell:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
6	CEBPB	chr12:40619419-40619781	Hela-S3	cervix:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
7	EBF1	chr12:40619613-40620945	GM12878	blood:	n/a	chr12:40620810-40620819
8	E2F4	chr12:40619625-40619821	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr12:40619438-40619732	HepG2	liver:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
11	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
12	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
13	TCF12	chr12:40617809-40619771	A549	lung:	n/a	chr12:40618605-40618615
14	REST	chr12:40618023-40619814	A549	lung:	n/a	chr12:40618846-40618856 chr12:40618853-40618866 chr12:40618751-40618761
15	TBP	chr12:40619440-40620658	GM12878	blood:	n/a	n/a
16	SPI1	chr12:40619630-40620808	GM12878	blood:	n/a	chr12:40620179-40620188
17	EP300	chr12:40619571-40620612	GM12878	blood:	n/a	chr12:40620580-40620589
18	CEBPB	chr12:40619408-40619855	A549	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
19	RELA	chr12:40618288-40619691	GM19099	blood:	n/a	n/a
20	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
21	CEBPB	chr12:40619102-40619954	A549	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
22	CEBPB	chr12:40619412-40619785	IMR90	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
23	STAT3	chr12:40619271-40619764	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr12:40619517-40619835	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr12:40619543-40619881	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
27	POLR2A	chr12:40618475-40620954	GM12878	blood:	n/a	n/a
28	MAX	chr12:40618017-40619722	A549	lung:	n/a	chr12:40618784-40618793
29	POLR2A	chr12:40616903-40621176	GM19193	blood:	n/a	n/a
30	CEBPB	chr12:40619453-40619682	K562	blood:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40615913..40618239-chr12:40619276..40621204,2	K562	blood:

Variant related genes	Relation type
ENSG00000225342	TF binding region
ENSG00000225342	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17489799	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518232	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17518665	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2404348	1.00[YRI][hapmap]
rs28370792	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
2	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
5	chr12:40617400-40619800	Active TSS	NHDF-Ad	bronchial
6	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
7	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:40617400-40621000	Active TSS	Right Atrium	heart
11	chr12:40617400-40621400	Active TSS	Aorta	Aorta
12	chr12:40617600-40619800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:40617600-40620200	Active TSS	Ovary	ovary
14	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
16	chr12:40617800-40620000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
18	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
19	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
20	chr12:40618000-40619800	Active TSS	Colonic Mucosa	Colon
21	chr12:40618000-40620400	Active TSS	Brain Substantia Nigra	brain
22	chr12:40618000-40620400	Active TSS	Psoas Muscle	Psoas
23	chr12:40618000-40620800	Active TSS	Lung	lung
24	chr12:40618000-40621000	Active TSS	A549	lung
25	chr12:40618200-40620000	Active TSS	Colon Smooth Muscle	Colon
26	chr12:40618200-40620600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr12:40618200-40620800	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:40618200-40620800	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr12:40618800-40620800	Flanking Active TSS	GM12878-XiMat	blood
30	chr12:40618800-40621200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:40619000-40619800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:40619000-40619800	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr12:40619000-40619800	Flanking Active TSS	Liver	Liver
34	chr12:40619000-40621000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:40619000-40621000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr12:40619200-40619800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:40619200-40620200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:40619200-40620200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr12:40619200-40620200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr12:40619200-40621200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr12:40619400-40619800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:40619400-40619800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:40619400-40620000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:40619400-40620000	Flanking Active TSS	NHLF	lung
45	chr12:40619400-40620200	Active TSS	Placenta	Placenta
46	chr12:40619400-40620200	Weak transcription	NH-A	brain
47	chr12:40619400-40620400	Weak transcription	Hela-S3	cervix
48	chr12:40619400-40620800	Active TSS	Brain Cingulate Gyrus	brain
49	chr12:40619400-40620800	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:40619400-40621000	Enhancers	HUVEC	blood vessel

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