Variant report

Variant	rs2592938
Chromosome Location	chr2:173830707-173830708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:173830560-173830710	GM12869	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:173830692-173830742	HNPCEpiC	eye:	n/a
2	chr2:173830692-173830742	HRCEpiC	kidney:	n/a
3	chr2:173830692-173830742	LNCaP	prostate:	n/a
4	chr2:173830692-173830742	NHDF-neo	bronchial:	n/a
5	chr2:173830692-173830742	H1-hESC	embryonic stem cell:	embryo
6	chr2:173830692-173830742	HIPEpiC	eye:	n/a
7	chr2:173830692-173830742	HRE	kidney:	n/a
8	chr2:173830692-173830742	NHBE	bronchial:	n/a
9	chr2:173830692-173830742	A549	lung:	n/a
10	chr2:173830692-173830742	Jurkat	blood:	n/a
11	chr2:173830692-173830742	HCM	heart:	n/a
12	chr2:173830692-173830742	SK-N-SH	brain:	n/a
13	chr2:173830692-173830742	AG10803	skin:	n/a
14	chr2:173830692-173830742	HL-60	blood:	n/a
15	chr2:173830692-173830742	Hela-S3	cervix:	n/a
16	chr2:173830692-173830742	GM19239	blood:	n/a
17	chr2:173830692-173830742	Caco-2	colon:	n/a
18	chr2:173830692-173830742	IMR90	lung:	fetal
19	chr2:173830692-173830742	PANC-1	pancreas:	n/a
20	chr2:173830692-173830742	AG09319	gingival:	n/a
21	chr2:173830692-173830742	HMEC	breast:	n/a
22	chr2:173830692-173830742	NT2-D1	testis:	n/a
23	chr2:173830692-173830742	MCF-7	breast:	n/a
24	chr2:173830692-173830742	U87	brain:	n/a
25	chr2:173830692-173830742	SAEC	small airway:	n/a
26	chr2:173830692-173830742	ProgFib	skin:	n/a
27	chr2:173830692-173830742	RPTEC	kidney:	n/a
28	chr2:173830692-173830742	HAEpiC	amniotic membrane:	n/a
29	chr2:173830692-173830742	HUVEC	blood vessel:	n/a
30	chr2:173830692-173830742	ovcar-3	ovarian:	n/a
31	chr2:173830692-173830742	NB4	blood:	n/a
32	chr2:173830692-173830742	GM12891	blood:	n/a
33	chr2:173830692-173830742	GM06990	blood:	n/a
34	chr2:173830692-173830742	HCT-116	colon:	n/a
35	chr2:173830692-173830742	ECC-1	luminal epithelium:	n/a
36	chr2:173830692-173830742	HEK293	kidney:	embryo
37	chr2:173830692-173830742	GM12878	blood:	n/a
38	chr2:173830692-173830742	PFSK-1	brain:	n/a
39	chr2:173830692-173830742	HCF	heart:	n/a
40	chr2:173830692-173830742	AG04449	skin:	fetal
41	chr2:173830692-173830742	HPAEpiC	pulmonary alveolar:	n/a
42	chr2:173830692-173830742	HRPEpiC	eye:	n/a
43	chr2:173830692-173830742	AG09309	skin:	n/a
44	chr2:173830692-173830742	AoSMC	blood vessel:	n/a
45	chr2:173830692-173830742	T-47D	breast:	n/a
46	chr2:173830692-173830742	Hepatocyte	liver:	n/a
47	chr2:173830692-173830742	HCPEpiC	choroid plexus:	n/a
48	chr2:173830692-173830742	SKMC	muscle:	n/a
49	chr2:173830692-173830742	PrEC	prostate:	n/a
50	chr2:173830692-173830742	BJ	skin:	n/a

No data

Variant related genes	Relation type
RAPGEF4	TF binding region
RAPGEF4	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1446980	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs1863174	1.00[MEX][hapmap]
rs2123506	0.81[AMR][1000 genomes]
rs2357807	1.00[MEX][hapmap]
rs2553004	1.00[MEX][hapmap]
rs2553014	1.00[MEX][hapmap]
rs2592940	1.00[MEX][hapmap]
rs2592945	0.81[AMR][1000 genomes]
rs2676503	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs2676516	1.00[MEX][hapmap]
rs2676527	1.00[MEX][hapmap]
rs2884283	1.00[MEX][hapmap]
rs4972866	1.00[MEX][hapmap]
rs7585729	1.00[MEX][hapmap]
rs7608030	1.00[EUR][1000 genomes]
rs930624	0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173807800-173831600	Weak transcription	Left Ventricle	heart
2	chr2:173816600-173831800	Weak transcription	Lung	lung
3	chr2:173822400-173835000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:173823000-173832200	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:173827000-173831600	Weak transcription	Pancreas	Pancrea
6	chr2:173827600-173832200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:173828000-173832400	Weak transcription	Hela-S3	cervix
8	chr2:173828000-173832600	Weak transcription	HMEC	breast
9	chr2:173828000-173833200	Weak transcription	Primary T cells from cord blood	blood
10	chr2:173828400-173831600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:173828400-173832800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:173828600-173833400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:173828600-173835600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:173829000-173842800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:173829200-173831800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:173829200-173832400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:173829200-173832800	Weak transcription	Aorta	Aorta
18	chr2:173829400-173831000	Weak transcription	HUVEC	blood vessel
19	chr2:173829400-173832000	Enhancers	Brain Germinal Matrix	brain
20	chr2:173829400-173832000	Weak transcription	Fetal Heart	heart
21	chr2:173829400-173834200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:173829600-173830800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:173829800-173832400	Weak transcription	NHDF-Ad	bronchial
24	chr2:173830000-173831600	Enhancers	Liver	Liver
25	chr2:173830200-173830800	Weak transcription	Thymus	Thymus
26	chr2:173830200-173832000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:173830200-173832000	Weak transcription	Fetal Brain Male	brain
28	chr2:173830400-173831600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:173830400-173831600	Weak transcription	Fetal Thymus	thymus
30	chr2:173830400-173831800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:173830400-173831800	Weak transcription	Brain Angular Gyrus	brain
32	chr2:173830400-173832000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:173830400-173832400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:173830400-173834400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:173830400-173840400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:173830600-173830800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:173830600-173831600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:173830600-173832000	Weak transcription	Brain Anterior Caudate	brain
39	chr2:173830600-173832200	Weak transcription	Fetal Intestine Small	intestine
40	chr2:173830600-173832400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:173830600-173832400	Enhancers	Adipose Nuclei	Adipose
42	chr2:173830600-173834200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links