Variant report

Variant	rs2583016
Chromosome Location	chr2:182545218-182545219
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	chr2:182545208-182545776	SK-N-SH	brain:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
2	MAX	chr2:182545130-182546027	H1-hESC	embryonic stem cell:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
3	ZNF143	chr2:182545205-182545898	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF263	chr2:182545063-182545669	HEK293-T-REx	kidney:	n/a	n/a
5	MAX	chr2:182545085-182545735	A549	lung:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
6	CREB1	chr2:182545145-182545622	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr2:182545091-182546434	H1-hESC	embryonic stem cell:	n/a	chr2:182545690-182545700 chr2:182546240-182546249
8	E2F6	chr2:182545082-182546025	H1-hESC	embryonic stem cell:	n/a	chr2:182545763-182545770 chr2:182545763-182545770 chr2:182545763-182545770
9	POLR2A	chr2:182544920-182545565	H1-neurons	neurons:	n/a	n/a
10	USF1	chr2:182545143-182545730	SK-N-SH_RA	brain:	n/a	n/a
11	MAX	chr2:182545162-182546012	H1-hESC	embryonic stem cell:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
12	SUZ12	chr2:182543491-182550280	NT2-D1	testis:	n/a	n/a
13	NRF1	chr2:182544976-182545766	SK-N-SH	brain:	n/a	n/a
14	SUZ12	chr2:182545142-182546680	H1-hESC	embryonic stem cell:	n/a	n/a
15	EGR1	chr2:182545102-182545297	K562	blood:	n/a	n/a
16	BACH1	chr2:182545187-182545744	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr2:182545208-182545775	H1-hESC	embryonic stem cell:	n/a	chr2:182545763-182545770 chr2:182545763-182545770 chr2:182545763-182545770
18	MXI1	chr2:182545186-182545729	H1-hESC	embryonic stem cell:	n/a	chr2:182545530-182545539
19	SIN3A	chr2:182545141-182546037	H1-hESC	embryonic stem cell:	n/a	chr2:182545530-182545539
20	NRF1	chr2:182545167-182545543	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTBP2	chr2:182545133-182546496	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr2:182545098-182546152	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:182545209-182545259	Jurkat	blood:	n/a
2	chr2:182545209-182545259	IMR90	lung:	fetal
3	chr2:182545209-182545259	A549	lung:	n/a
4	chr2:182545209-182545259	HNPCEpiC	eye:	n/a
5	chr2:182545209-182545259	HCT-116	colon:	n/a
6	chr2:182545209-182545259	AG09309	skin:	n/a
7	chr2:182545209-182545259	BJ	skin:	n/a
8	chr2:182545209-182545259	GM12878	blood:	n/a
9	chr2:182545209-182545259	HPAEpiC	pulmonary alveolar:	n/a
10	chr2:182545209-182545259	HRE	kidney:	n/a
11	chr2:182545209-182545259	HEEpiC	esophagus:	n/a
12	chr2:182545209-182545259	ovcar-3	ovarian:	n/a
13	chr2:182545209-182545259	H1-hESC	embryonic stem cell:	embryo
14	chr2:182545209-182545259	GM12891	blood:	n/a
15	chr2:182545209-182545259	HepG2	liver:	n/a
16	chr2:182545209-182545259	ECC-1	luminal epithelium:	n/a
17	chr2:182545209-182545259	K562	blood:	n/a
18	chr2:182545209-182545259	HCPEpiC	choroid plexus:	n/a
19	chr2:182545209-182545259	Caco-2	colon:	n/a
20	chr2:182545209-182545259	Hela-S3	cervix:	n/a
21	chr2:182545209-182545259	GM19239	blood:	n/a
22	chr2:182545209-182545259	PANC-1	pancreas:	n/a
23	chr2:182545209-182545259	LNCaP	prostate:	n/a
24	chr2:182545209-182545259	NHDF-neo	bronchial:	n/a
25	chr2:182545209-182545259	HMEC	breast:	n/a
26	chr2:182545209-182545259	GM06990	blood:	n/a
27	chr2:182545209-182545259	BE2_C	brain:	n/a
28	chr2:182545209-182545259	HUVEC	blood vessel:	n/a
29	chr2:182545209-182545259	AG09319	gingival:	n/a
30	chr2:182545209-182545259	PrEC	prostate:	n/a
31	chr2:182545209-182545259	HEK293	kidney:	embryo
32	chr2:182545209-182545259	NT2-D1	testis:	n/a
33	chr2:182545209-182545259	HIPEpiC	eye:	n/a
34	chr2:182545209-182545259	MCF-7	breast:	n/a
35	chr2:182545209-182545259	SAEC	small airway:	n/a
36	chr2:182545209-182545259	SK-N-MC	brain:	n/a
37	chr2:182545209-182545259	Hepatocyte	liver:	n/a
38	chr2:182545209-182545259	ProgFib	skin:	n/a
39	chr2:182545209-182545259	HL-60	blood:	n/a
40	chr2:182545209-182545259	SKMC	muscle:	n/a
41	chr2:182545209-182545259	AG10803	skin:	n/a
42	chr2:182545209-182545259	RPTEC	kidney:	n/a
43	chr2:182545209-182545259	NB4	blood:	n/a
44	chr2:182545209-182545259	T-47D	breast:	n/a
45	chr2:182545209-182545259	AG04449	skin:	fetal
46	chr2:182545209-182545259	GM12892	blood:	n/a
47	chr2:182545209-182545259	HAEpiC	amniotic membrane:	n/a
48	chr2:182545209-182545259	CMK	blood:	n/a
49	chr2:182545209-182545259	MCF10A-Er-Src	breast:	n/a
50	chr2:182545209-182545259	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:182542601..182545361-chr2:182546496..182548838,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CERKL-4	chr2:182545157-182545274	NONHSAT075879

Variant related genes	Relation type
ENSG00000234595	TF binding region
ENSG00000234595	CpG island
ENSG00000234595	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10201723	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes]
rs13032839	0.82[EUR][1000 genomes]
rs1372120	0.83[EUR][1000 genomes]
rs17198745	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17270924	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17270931	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967351	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2368223	0.83[EUR][1000 genomes]
rs3910660	0.81[EUR][1000 genomes]
rs3910663	0.83[EUR][1000 genomes]
rs3910664	0.89[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4666571	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4666791	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4666793	0.91[EUR][1000 genomes]
rs62190012	0.91[EUR][1000 genomes]
rs7596272	0.90[EUR][1000 genomes]
rs7602326	0.83[EUR][1000 genomes]
rs935087	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv834477	chr2:182438121-182593527	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2583016	PDE11A	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182542400-182545400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
2	chr2:182542400-182546200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
3	chr2:182543000-182545600	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr2:182543600-182550200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:182544000-182545600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
6	chr2:182544200-182545600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:182544800-182545600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:182544800-182545600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr2:182545000-182545400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
10	chr2:182545000-182545400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:182545000-182545400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:182545000-182545400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:182545000-182545400	Bivalent Enhancer	Fetal Intestine Large	intestine
14	chr2:182545000-182545600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
15	chr2:182545000-182545600	Bivalent/Poised TSS	A549	lung
16	chr2:182545000-182545800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:182545000-182545800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:182545000-182545800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:182545000-182545800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:182545000-182546000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:182545000-182546200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:182545000-182546200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:182545000-182546200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr2:182545000-182547200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr2:182545000-182548000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:182545000-182548400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
27	chr2:182545200-182545400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:182545200-182545400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:182545200-182545400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
30	chr2:182545200-182545400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:182545200-182545400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:182545200-182545400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
33	chr2:182545200-182545400	Bivalent Enhancer	Right Ventricle	heart
34	chr2:182545200-182545400	Bivalent Enhancer	Thymus	Thymus
35	chr2:182545200-182545400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
36	chr2:182545200-182545600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:182545200-182545600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:182545200-182545600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr2:182545200-182545600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
40	chr2:182545200-182545600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
41	chr2:182545200-182545600	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr2:182545200-182545600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr2:182545200-182545600	Bivalent Enhancer	Fetal Stomach	stomach
44	chr2:182545200-182545600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
45	chr2:182545200-182545800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
46	chr2:182545200-182545800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr2:182545200-182545800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:182545200-182545800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:182545200-182545800	Enhancers	Right Atrium	heart
50	chr2:182545200-182545800	Bivalent/Poised TSS	NHLF	lung

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