Variant report

Variant	rs1004478
Chromosome Location	chr2:234825895-234825896
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:234825859-234825909	HepG2	liver:	n/a
2	chr2:234825859-234825909	CMK	blood:	n/a
3	chr2:234825859-234825909	PrEC	prostate:	n/a
4	chr2:234825859-234825909	HMEC	breast:	n/a
5	chr2:234825859-234825909	MCF10A-Er-Src	breast:	n/a
6	chr2:234825859-234825909	HIPEpiC	eye:	n/a
7	chr2:234825859-234825909	MCF-7	breast:	n/a
8	chr2:234825859-234825909	H1-hESC	embryonic stem cell:	embryo
9	chr2:234825859-234825909	LNCaP	prostate:	n/a
10	chr2:234825859-234825909	AG10803	skin:	n/a
11	chr2:234825859-234825909	SK-N-MC	brain:	n/a
12	chr2:234825859-234825909	SAEC	small airway:	n/a
13	chr2:234825859-234825909	NH-A	brain:	n/a
14	chr2:234825859-234825909	A549	lung:	n/a
15	chr2:234825859-234825909	T-47D	breast:	n/a
16	chr2:234825859-234825909	PFSK-1	brain:	n/a
17	chr2:234825859-234825909	SK-N-SH_RA	brain:	n/a
18	chr2:234825859-234825909	NHBE	bronchial:	n/a
19	chr2:234825859-234825909	HCF	heart:	n/a
20	chr2:234825859-234825909	PANC-1	pancreas:	n/a
21	chr2:234825859-234825909	K562	blood:	n/a
22	chr2:234825859-234825909	ovcar-3	ovarian:	n/a
23	chr2:234825859-234825909	BE2_C	brain:	n/a
24	chr2:234825859-234825909	AoSMC	blood vessel:	n/a
25	chr2:234825859-234825909	ECC-1	luminal epithelium:	n/a
26	chr2:234825859-234825909	AG04450	lung:	fetal
27	chr2:234825859-234825909	HRCEpiC	kidney:	n/a
28	chr2:234825859-234825909	RPTEC	kidney:	n/a
29	chr2:234825859-234825909	Hela-S3	cervix:	n/a
30	chr2:234825859-234825909	HAEpiC	amniotic membrane:	n/a
31	chr2:234825859-234825909	AG09309	skin:	n/a
32	chr2:234825859-234825909	HEEpiC	esophagus:	n/a
33	chr2:234825859-234825909	HCPEpiC	choroid plexus:	n/a
34	chr2:234825859-234825909	GM12878	blood:	n/a
35	chr2:234825859-234825909	HRPEpiC	eye:	n/a
36	chr2:234825859-234825909	NHDF-neo	bronchial:	n/a
37	chr2:234825859-234825909	NB4	blood:	n/a
38	chr2:234825859-234825909	HNPCEpiC	eye:	n/a
39	chr2:234825859-234825909	AG04449	skin:	fetal
40	chr2:234825859-234825909	HPAEpiC	pulmonary alveolar:	n/a
41	chr2:234825859-234825909	NT2-D1	testis:	n/a
42	chr2:234825859-234825909	GM12892	blood:	n/a
43	chr2:234825859-234825909	Hepatocyte	liver:	n/a
44	chr2:234825859-234825909	HRE	kidney:	n/a
45	chr2:234825859-234825909	U87	brain:	n/a
46	chr2:234825859-234825909	Jurkat	blood:	n/a
47	chr2:234825859-234825909	HEK293	kidney:	embryo
48	chr2:234825859-234825909	HCT-116	colon:	n/a
49	chr2:234825859-234825909	SKMC	muscle:	n/a
50	chr2:234825859-234825909	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234761504..234764477-chr2:234824983..234827662,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRPM8	CpG island
ENSG00000123485	Chromatin interaction

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

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

rs_ID	r²[population]
rs10490010	0.93[CEU][hapmap]
rs10803665	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10803666	0.93[CEU][hapmap]
rs10929317	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11562941	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11562954	0.93[CEU][hapmap]
rs12473889	0.93[CEU][hapmap]
rs12988953	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028228	0.93[CEU][hapmap]
rs17862920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862921	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17863838	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17863841	0.93[CEU][hapmap]
rs17863842	0.93[CEU][hapmap]
rs17864738	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17864741	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28901590	0.80[YRI][hapmap]
rs28901597	0.85[YRI][hapmap]
rs35168608	0.85[EUR][1000 genomes]
rs6717978	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6717992	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6741751	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7558436	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7562952	0.93[CEU][hapmap]
rs7562971	0.93[CEU][hapmap]
rs7577262	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9646718	1.00[CEU][hapmap];0.97[EUR][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234825000-234826000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:234825000-234827200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234825600-234826000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:234825800-234826000	Enhancers	Brain Germinal Matrix	brain
5	chr2:234825800-234826200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:234825800-234826200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr2:234825800-234826200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr2:234825800-234826400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:234825800-234826600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:234825800-234826600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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