Variant report

Variant	rs2723273
Chromosome Location	chr12:40619301-40619302
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	POLR2A	chr12:40618944-40619600	PFSK-1	brain:	n/a	n/a
3	MAZ	chr12:40617778-40619458	IMR90	lung:	n/a	chr12:40618784-40618793
4	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
5	KAP1	chr12:40618416-40619717	HEK293	kidney:	n/a	n/a
6	MXI1	chr12:40618586-40619319	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:40617796-40619536	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF263	chr12:40617969-40619401	HEK293-T-REx	kidney:	n/a	chr12:40618700-40618709 chr12:40619158-40619167 chr12:40618762-40618771
9	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
10	RELA	chr12:40617863-40619486	GM18951	blood:	n/a	n/a
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	STAT3	chr12:40619239-40619482	MCF10A-Er-Src	breast:	n/a	n/a
16	GATA3	chr12:40618121-40619606	A549	lung:	n/a	n/a
17	GATA2	chr12:40617993-40619425	SH-SY5Y	brain:	n/a	chr12:40618106-40618116
18	MAZ	chr12:40617948-40619513	GM12878	blood:	n/a	chr12:40618784-40618793
19	RELA	chr12:40618288-40619691	GM19099	blood:	n/a	n/a
20	BHLHE40	chr12:40618428-40619399	GM12878	blood:	n/a	chr12:40618496-40618512 chr12:40618745-40618761 chr12:40618493-40618509 chr12:40618858-40618874
21	MAX	chr12:40618149-40619647	A549	lung:	n/a	chr12:40618784-40618793
22	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
23	WRNIP1	chr12:40619023-40619584	GM12878	blood:	n/a	n/a
24	CTCF	chr12:40619280-40619430	AG10803	skin:	n/a	n/a
25	CEBPB	chr12:40619102-40619954	A549	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
26	MAX	chr12:40618309-40619407	NB4	blood:	n/a	chr12:40618784-40618793
27	CTCF	chr12:40619260-40619410	NHLF	lung:	n/a	n/a
28	STAT3	chr12:40619271-40619764	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
30	POLR2A	chr12:40618182-40619560	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr12:40618475-40620954	GM12878	blood:	n/a	n/a
32	MAX	chr12:40618017-40619722	A549	lung:	n/a	chr12:40618784-40618793
33	POLR2A	chr12:40616903-40621176	GM19193	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:40619282-40619332	Hepatocyte	liver:	n/a
2	chr12:40619282-40619332	CMK	blood:	n/a
3	chr12:40619282-40619332	NB4	blood:	n/a
4	chr12:40619282-40619332	T-47D	breast:	n/a
5	chr12:40619282-40619332	HCT-116	colon:	n/a
6	chr12:40619282-40619332	SKMC	muscle:	n/a
7	chr12:40619282-40619332	AG09309	skin:	n/a
8	chr12:40619282-40619332	NHDF-neo	bronchial:	n/a
9	chr12:40619282-40619332	AG04449	skin:	fetal
10	chr12:40619282-40619332	H1-hESC	embryonic stem cell:	embryo
11	chr12:40619282-40619332	SK-N-MC	brain:	n/a
12	chr12:40619282-40619332	HCPEpiC	choroid plexus:	n/a
13	chr12:40619282-40619332	NH-A	brain:	n/a
14	chr12:40619282-40619332	AG10803	skin:	n/a
15	chr12:40619282-40619332	GM12892	blood:	n/a
16	chr12:40619282-40619332	LNCaP	prostate:	n/a
17	chr12:40619282-40619332	HCM	heart:	n/a
18	chr12:40619282-40619332	Caco-2	colon:	n/a
19	chr12:40619282-40619332	GM06990	blood:	n/a
20	chr12:40619282-40619332	HUVEC	blood vessel:	n/a
21	chr12:40619282-40619332	NHBE	bronchial:	n/a
22	chr12:40619282-40619332	GM19239	blood:	n/a
23	chr12:40619282-40619332	MCF10A-Er-Src	breast:	n/a
24	chr12:40619282-40619332	SK-N-SH	brain:	n/a
25	chr12:40619282-40619332	BE2_C	brain:	n/a
26	chr12:40619282-40619332	AG09319	gingival:	n/a
27	chr12:40619282-40619332	HEEpiC	esophagus:	n/a
28	chr12:40619282-40619332	U87	brain:	n/a
29	chr12:40619282-40619332	SAEC	small airway:	n/a
30	chr12:40619282-40619332	A549	lung:	n/a
31	chr12:40619282-40619332	PANC-1	pancreas:	n/a
32	chr12:40619282-40619332	PFSK-1	brain:	n/a
33	chr12:40619282-40619332	HMEC	breast:	n/a
34	chr12:40619282-40619332	Hela-S3	cervix:	n/a
35	chr12:40619282-40619332	GM12878	blood:	n/a
36	chr12:40619282-40619332	HNPCEpiC	eye:	n/a
37	chr12:40619282-40619332	HIPEpiC	eye:	n/a
38	chr12:40619282-40619332	HepG2	liver:	n/a
39	chr12:40619282-40619332	AG04450	lung:	fetal
40	chr12:40619282-40619332	HL-60	blood:	n/a
41	chr12:40619282-40619332	ECC-1	luminal epithelium:	n/a
42	chr12:40619282-40619332	HPAEpiC	pulmonary alveolar:	n/a
43	chr12:40619282-40619332	SK-N-SH_RA	brain:	n/a
44	chr12:40619282-40619332	IMR90	lung:	fetal
45	chr12:40619282-40619332	MCF-7	breast:	n/a
46	chr12:40619282-40619332	HRE	kidney:	n/a
47	chr12:40619282-40619332	HAEpiC	amniotic membrane:	n/a
48	chr12:40619282-40619332	HEK293	kidney:	embryo
49	chr12:40619282-40619332	NT2-D1	testis:	n/a
50	chr12:40619282-40619332	HCF	heart:	n/a

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
LRRK2	TF binding region
ENSG00000225342	CpG island
LRRK2	CpG island
ENSG00000225342	Chromatin interaction

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

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

rs_ID	r²[population]
rs17458121	1.00[CHB][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]
rs2252434	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256286	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256408	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2638273	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708405	1.00[CEU][hapmap]
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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2723272	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs28365686	1.00[CEU][hapmap]
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:112 , 50 per page) page: 1 2 3

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	chr12:40617400-40619400	Active TSS	Small Intestine	intestine
6	chr12:40617400-40619600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:40617400-40619800	Active TSS	NHDF-Ad	bronchial
8	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
9	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:40617400-40621000	Active TSS	Right Atrium	heart
13	chr12:40617400-40621400	Active TSS	Aorta	Aorta
14	chr12:40617600-40619800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr12:40617600-40620200	Active TSS	Ovary	ovary
16	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
18	chr12:40617800-40619400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
19	chr12:40617800-40619400	Active TSS	NHLF	lung
20	chr12:40617800-40619600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr12:40617800-40619600	Active TSS	Right Ventricle	heart
22	chr12:40617800-40620000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
24	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
25	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
26	chr12:40618000-40619400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr12:40618000-40619400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr12:40618000-40619400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:40618000-40619400	Active TSS	NH-A	brain
30	chr12:40618000-40619600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:40618000-40619600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr12:40618000-40619600	Active TSS	Esophagus	oesophagus
33	chr12:40618000-40619600	Active TSS	Fetal Muscle Trunk	muscle
34	chr12:40618000-40619600	Active TSS	Left Ventricle	heart
35	chr12:40618000-40619600	Bivalent/Poised TSS	Thymus	Thymus
36	chr12:40618000-40619600	Flanking Active TSS	HMEC	breast
37	chr12:40618000-40619800	Active TSS	Colonic Mucosa	Colon
38	chr12:40618000-40620400	Active TSS	Brain Substantia Nigra	brain
39	chr12:40618000-40620400	Active TSS	Psoas Muscle	Psoas
40	chr12:40618000-40620800	Active TSS	Lung	lung
41	chr12:40618000-40621000	Active TSS	A549	lung
42	chr12:40618200-40619400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr12:40618200-40619400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr12:40618200-40619400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr12:40618200-40619400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:40618200-40619400	Active TSS	Spleen	Spleen
47	chr12:40618200-40619600	Active TSS	Fetal Stomach	stomach
48	chr12:40618200-40619600	Bivalent/Poised TSS	Fetal Thymus	thymus
49	chr12:40618200-40619600	Active TSS	Pancreas	Pancrea
50	chr12:40618200-40619600	Active TSS	Sigmoid Colon	Sigmoid Colon

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