Variant report

Variant	rs2491259
Chromosome Location	chr1:221056674-221056675
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:221055626-221056898	HL-60	blood:	n/a	n/a
2	MAZ	chr1:221051935-221057120	IMR90	lung:	n/a	chr1:221052899-221052909 chr1:221052464-221052473 chr1:221052603-221052613
3	POLR2A	chr1:221054077-221056927	HL-60	blood:	n/a	n/a
4	CEBPB	chr1:221056567-221056720	H1-hESC	embryonic stem cell:	n/a	chr1:221056602-221056615 chr1:221056604-221056615

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:221056674-221056724	HCT-116	colon:	n/a
2	chr1:221056674-221056724	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:221056674-221056724	IMR90	lung:	fetal
4	chr1:221056674-221056724	AG04450	lung:	fetal
5	chr1:221056674-221056724	HNPCEpiC	eye:	n/a
6	chr1:221056674-221056724	HCPEpiC	choroid plexus:	n/a
7	chr1:221056674-221056724	NT2-D1	testis:	n/a
8	chr1:221056674-221056724	HEK293	kidney:	embryo
9	chr1:221056674-221056724	Caco-2	colon:	n/a
10	chr1:221056674-221056724	HAEpiC	amniotic membrane:	n/a
11	chr1:221056674-221056724	SK-N-SH_RA	brain:	n/a
12	chr1:221056674-221056724	SKMC	muscle:	n/a
13	chr1:221056674-221056724	NH-A	brain:	n/a
14	chr1:221056674-221056724	T-47D	breast:	n/a
15	chr1:221056674-221056724	GM06990	blood:	n/a
16	chr1:221056674-221056724	RPTEC	kidney:	n/a
17	chr1:221056674-221056724	U87	brain:	n/a
18	chr1:221056674-221056724	AG09309	skin:	n/a
19	chr1:221056674-221056724	HL-60	blood:	n/a
20	chr1:221056674-221056724	A549	lung:	n/a
21	chr1:221056674-221056724	BJ	skin:	n/a
22	chr1:221056674-221056724	Hela-S3	cervix:	n/a
23	chr1:221056674-221056724	AG09319	gingival:	n/a
24	chr1:221056674-221056724	HepG2	liver:	n/a
25	chr1:221056674-221056724	Hepatocyte	liver:	n/a
26	chr1:221056674-221056724	BE2_C	brain:	n/a
27	chr1:221056674-221056724	MCF-7	breast:	n/a
28	chr1:221056674-221056724	HRPEpiC	eye:	n/a
29	chr1:221056674-221056724	HEEpiC	esophagus:	n/a
30	chr1:221056674-221056724	HMEC	breast:	n/a
31	chr1:221056674-221056724	HRCEpiC	kidney:	n/a
32	chr1:221056674-221056724	LNCaP	prostate:	n/a
33	chr1:221056674-221056724	HRE	kidney:	n/a
34	chr1:221056674-221056724	AG04449	skin:	fetal
35	chr1:221056674-221056724	NHDF-neo	bronchial:	n/a
36	chr1:221056674-221056724	ProgFib	skin:	n/a
37	chr1:221056674-221056724	AoSMC	blood vessel:	n/a
38	chr1:221056674-221056724	CMK	blood:	n/a
39	chr1:221056674-221056724	GM12878	blood:	n/a
40	chr1:221056674-221056724	SK-N-MC	brain:	n/a
41	chr1:221056674-221056724	PANC-1	pancreas:	n/a
42	chr1:221056674-221056724	SAEC	small airway:	n/a
43	chr1:221056674-221056724	Jurkat	blood:	n/a
44	chr1:221056674-221056724	SK-N-SH	brain:	n/a
45	chr1:221056674-221056724	NHBE	bronchial:	n/a
46	chr1:221056674-221056724	GM19239	blood:	n/a
47	chr1:221056674-221056724	ECC-1	luminal epithelium:	n/a
48	chr1:221056674-221056724	PFSK-1	brain:	n/a
49	chr1:221056674-221056724	HCF	heart:	n/a
50	chr1:221056674-221056724	K562	blood:	n/a

No data

Variant related genes	Relation type
HLA-AS1	TF binding region
HLA-AS1	CpG island

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2738749	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738754	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2807857	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868058	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1798350	chr1:221020278-221069740	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2491259	RP11-295M18.2	cis	Artery Tibial	GTEx
rs2491259	RP11-295M18.2	cis	Nerve Tibial	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221052000-221058000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr1:221053600-221057400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:221054800-221057400	Weak transcription	Gastric	stomach
4	chr1:221054800-221057600	Weak transcription	HSMMtube	muscle
5	chr1:221054800-221058400	Weak transcription	K562	blood
6	chr1:221054800-221061000	Weak transcription	HSMM	muscle
7	chr1:221055000-221056800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr1:221055000-221056800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr1:221055000-221057000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
10	chr1:221055000-221058800	Weak transcription	Ovary	ovary
11	chr1:221055800-221056800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:221055800-221057600	Weak transcription	Pancreas	Pancrea
13	chr1:221055800-221057800	Strong transcription	Spleen	Spleen
14	chr1:221055800-221058000	Weak transcription	Psoas Muscle	Psoas
15	chr1:221055800-221060400	Weak transcription	Hela-S3	cervix
16	chr1:221056000-221056800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:221056000-221057200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:221056000-221057200	Weak transcription	Esophagus	oesophagus
19	chr1:221056000-221057200	Strong transcription	Left Ventricle	heart
20	chr1:221056000-221057200	Active TSS	Rectal Smooth Muscle	rectum
21	chr1:221056000-221057200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:221056000-221057200	Weak transcription	HUVEC	blood vessel
23	chr1:221056000-221057400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:221056000-221057400	Strong transcription	Right Ventricle	heart
25	chr1:221056000-221057600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:221056000-221057600	Weak transcription	Aorta	Aorta
27	chr1:221056000-221057800	Genic enhancers	Liver	Liver
28	chr1:221056000-221058000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:221056000-221058000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:221056000-221061000	Weak transcription	NHDF-Ad	bronchial
31	chr1:221056200-221056800	Enhancers	Primary B cells from cord blood	blood
32	chr1:221056200-221057000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:221056200-221057200	Weak transcription	Lung	lung
34	chr1:221056200-221057600	Genic enhancers	Adipose Nuclei	Adipose
35	chr1:221056200-221058000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
36	chr1:221056200-221058600	Bivalent Enhancer	Fetal Stomach	stomach
37	chr1:221056200-221059200	Strong transcription	Osteobl	bone
38	chr1:221056200-221060400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:221056400-221056800	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr1:221056400-221056800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
41	chr1:221056400-221057000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr1:221056400-221057000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:221056400-221057000	Enhancers	NHLF	lung
44	chr1:221056400-221057200	Enhancers	Primary hematopoietic stem cells	blood
45	chr1:221056400-221057400	Weak transcription	Right Atrium	heart
46	chr1:221056400-221059000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr1:221056400-221060200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:221056600-221056800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr1:221056600-221057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:221056600-221057000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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