Variant report

Variant	rs2256408
Chromosome Location	chr12:40619082-40619083
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	MAX	chr12:40618439-40619254	GM12878	blood:	n/a	chr12:40618784-40618793
2	POLR2A	chr12:40618944-40619600	PFSK-1	brain:	n/a	n/a
3	BCLAF1	chr12:40618574-40619091	GM12878	blood:	n/a	chr12:40618849-40618857 chr12:40618818-40618831
4	MAZ	chr12:40617778-40619458	IMR90	lung:	n/a	chr12:40618784-40618793
5	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
6	KAP1	chr12:40618416-40619717	HEK293	kidney:	n/a	n/a
7	MXI1	chr12:40618586-40619319	GM12878	blood:	n/a	n/a
8	MAX	chr12:40618710-40619144	HepG2	liver:	n/a	chr12:40618784-40618793
9	POLR2A	chr12:40618400-40619177	GM12878	blood:	n/a	n/a
10	MAX	chr12:40618572-40619163	MCF-7	breast:	n/a	chr12:40618784-40618793
11	MAX	chr12:40618529-40619188	H1-hESC	embryonic stem cell:	n/a	chr12:40618784-40618793
12	POLR2A	chr12:40618261-40619101	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr12:40617796-40619536	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F6	chr12:40618311-40619198	H1-hESC	embryonic stem cell:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
15	CTCF	chr12:40618960-40619110	RPTEC	kidney:	n/a	n/a
16	EP300	chr12:40618532-40619121	T-47D	breast:	n/a	n/a
17	MAX	chr12:40618379-40619285	ECC-1	luminal epithelium:	n/a	chr12:40618784-40618793
18	E2F6	chr12:40618219-40619269	H1-hESC	embryonic stem cell:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
19	ZNF263	chr12:40617969-40619401	HEK293-T-REx	kidney:	n/a	chr12:40618700-40618709 chr12:40619158-40619167 chr12:40618762-40618771
20	MAX	chr12:40618215-40619232	ECC-1	luminal epithelium:	n/a	chr12:40618784-40618793
21	E2F6	chr12:40618259-40619239	A549	lung:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
22	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
23	RELA	chr12:40617863-40619486	GM18951	blood:	n/a	n/a
24	EBF1	chr12:40618548-40619109	GM12878	blood:	n/a	chr12:40618843-40618852 chr12:40618843-40618852
25	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
26	POLR2A	chr12:40618322-40619091	NB4	blood:	n/a	n/a
27	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
28	TBP	chr12:40618642-40619093	GM12878	blood:	n/a	n/a
29	TCF12	chr12:40617809-40619771	A549	lung:	n/a	chr12:40618605-40618615
30	CTCF	chr12:40618960-40619110	A549	lung:	n/a	n/a
31	POLR2A	chr12:40618185-40619094	ECC-1	luminal epithelium:	n/a	n/a
32	REST	chr12:40618351-40619176	HL-60	blood:	n/a	chr12:40618846-40618856 chr12:40618853-40618866 chr12:40618751-40618761
33	TCF12	chr12:40618263-40619269	ECC-1	luminal epithelium:	n/a	chr12:40618605-40618615
34	REST	chr12:40618023-40619814	A549	lung:	n/a	chr12:40618846-40618856 chr12:40618853-40618866 chr12:40618751-40618761
35	E2F6	chr12:40618338-40619118	A549	lung:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
36	POLR2A	chr12:40618309-40619102	HL-60	blood:	n/a	n/a
37	CTCF	chr12:40619020-40619170	HA-sp	spinal cord:	n/a	n/a
38	YY1	chr12:40618693-40619115	ECC-1	luminal epithelium:	n/a	chr12:40618853-40618867 chr12:40618806-40618820
39	CHD2	chr12:40618314-40619207	GM12878	blood:	n/a	chr12:40618748-40618758
40	EP300	chr12:40618206-40619187	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr12:40618157-40619089	PFSK-1	brain:	n/a	n/a
42	TBL1XR1	chr12:40618638-40619172	GM12878	blood:	n/a	n/a
43	MAX	chr12:40618828-40619100	H1-hESC	embryonic stem cell:	n/a	n/a
44	GATA3	chr12:40618121-40619606	A549	lung:	n/a	n/a
45	EBF1	chr12:40618343-40619132	GM12878	blood:	n/a	chr12:40618843-40618852 chr12:40618843-40618852
46	GATA2	chr12:40617993-40619425	SH-SY5Y	brain:	n/a	chr12:40618106-40618116
47	TAF1	chr12:40618135-40619154	ECC-1	luminal epithelium:	n/a	n/a
48	MAZ	chr12:40617948-40619513	GM12878	blood:	n/a	chr12:40618784-40618793
49	POLR2A	chr12:40618239-40619135	A549	lung:	n/a	n/a
50	POU2F2	chr12:40618408-40619130	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRRK2	TF binding region
ENSG00000225342	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1352878	1.00[MEX][hapmap];0.87[MKK][hapmap]
rs1352879	1.00[MEX][hapmap];0.87[MKK][hapmap]
rs17489344	1.00[AMR][1000 genomes]
rs17489764	1.00[AMR][1000 genomes]
rs17490062	1.00[AMR][1000 genomes]
rs17490397	0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518532	1.00[AMR][1000 genomes]
rs17518910	1.00[AMR][1000 genomes]
rs17519034	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2249281	1.00[MEX][hapmap]
rs2252434	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256286	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2638273	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708439	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708440	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708444	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs2723256	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2723262	0.84[AFR][1000 genomes]
rs2723266	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2723267	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2723272	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs2723273	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370790	1.00[AMR][1000 genomes]
rs28370793	1.00[AMR][1000 genomes]
rs7978216	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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40619200	Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
3	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
6	chr12:40617400-40619200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:40617400-40619400	Active TSS	Small Intestine	intestine
8	chr12:40617400-40619600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:40617400-40619800	Active TSS	NHDF-Ad	bronchial
10	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
11	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:40617400-40621000	Active TSS	Right Atrium	heart
15	chr12:40617400-40621400	Active TSS	Aorta	Aorta
16	chr12:40617600-40619800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr12:40617600-40620200	Active TSS	Ovary	ovary
18	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
20	chr12:40617800-40619200	Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr12:40617800-40619400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
22	chr12:40617800-40619400	Active TSS	NHLF	lung
23	chr12:40617800-40619600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr12:40617800-40619600	Active TSS	Right Ventricle	heart
25	chr12:40617800-40620000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
27	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
28	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
29	chr12:40618000-40619200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:40618000-40619200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr12:40618000-40619200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:40618000-40619200	Active TSS	Adipose Nuclei	Adipose
33	chr12:40618000-40619200	Active TSS	Brain Germinal Matrix	brain
34	chr12:40618000-40619200	Active TSS	Fetal Brain Female	brain
35	chr12:40618000-40619200	Active TSS	Hela-S3	cervix
36	chr12:40618000-40619400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr12:40618000-40619400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr12:40618000-40619400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:40618000-40619400	Active TSS	NH-A	brain
40	chr12:40618000-40619600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr12:40618000-40619600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr12:40618000-40619600	Active TSS	Esophagus	oesophagus
43	chr12:40618000-40619600	Active TSS	Fetal Muscle Trunk	muscle
44	chr12:40618000-40619600	Active TSS	Left Ventricle	heart
45	chr12:40618000-40619600	Bivalent/Poised TSS	Thymus	Thymus
46	chr12:40618000-40619600	Flanking Active TSS	HMEC	breast
47	chr12:40618000-40619800	Active TSS	Colonic Mucosa	Colon
48	chr12:40618000-40620400	Active TSS	Brain Substantia Nigra	brain
49	chr12:40618000-40620400	Active TSS	Psoas Muscle	Psoas
50	chr12:40618000-40620800	Active TSS	Lung	lung

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