Variant report

Variant	rs7489259
Chromosome Location	chr12:47221078-47221079
allele	C/T
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:0)
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	chr12:47221046-47221096	BE2_C	brain:	n/a
2	chr12:47221046-47221096	NH-A	brain:	n/a
3	chr12:47221046-47221096	PANC-1	pancreas:	n/a
4	chr12:47221046-47221096	SK-N-SH_RA	brain:	n/a
5	chr12:47221046-47221096	HEEpiC	esophagus:	n/a
6	chr12:47221046-47221096	HCM	heart:	n/a
7	chr12:47221046-47221096	HRCEpiC	kidney:	n/a
8	chr12:47221046-47221096	CMK	blood:	n/a
9	chr12:47221046-47221096	HRPEpiC	eye:	n/a
10	chr12:47221046-47221096	HL-60	blood:	n/a
11	chr12:47221046-47221096	PrEC	prostate:	n/a
12	chr12:47221046-47221096	GM06990	blood:	n/a
13	chr12:47221046-47221096	BJ	skin:	n/a
14	chr12:47221046-47221096	HAEpiC	amniotic membrane:	n/a
15	chr12:47221046-47221096	HIPEpiC	eye:	n/a
16	chr12:47221046-47221096	AG10803	skin:	n/a
17	chr12:47221046-47221096	ECC-1	luminal epithelium:	n/a
18	chr12:47221046-47221096	HepG2	liver:	n/a
19	chr12:47221046-47221096	HUVEC	blood vessel:	n/a
20	chr12:47221046-47221096	GM12891	blood:	n/a
21	chr12:47221046-47221096	HPAEpiC	pulmonary alveolar:	n/a
22	chr12:47221046-47221096	HMEC	breast:	n/a
23	chr12:47221046-47221096	GM12878	blood:	n/a
24	chr12:47221046-47221096	NB4	blood:	n/a
25	chr12:47221046-47221096	Caco-2	colon:	n/a
26	chr12:47221046-47221096	A549	lung:	n/a
27	chr12:47221046-47221096	HEK293	kidney:	embryo
28	chr12:47221046-47221096	GM12892	blood:	n/a
29	chr12:47221046-47221096	AG09319	gingival:	n/a
30	chr12:47221046-47221096	NHDF-neo	bronchial:	n/a
31	chr12:47221046-47221096	PFSK-1	brain:	n/a
32	chr12:47221046-47221096	SK-N-SH	brain:	n/a
33	chr12:47221046-47221096	H1-hESC	embryonic stem cell:	embryo
34	chr12:47221046-47221096	AG04450	lung:	fetal
35	chr12:47221046-47221096	RPTEC	kidney:	n/a
36	chr12:47221046-47221096	MCF-7	breast:	n/a
37	chr12:47221046-47221096	SAEC	small airway:	n/a
38	chr12:47221046-47221096	HCF	heart:	n/a
39	chr12:47221046-47221096	Hela-S3	cervix:	n/a
40	chr12:47221046-47221096	HNPCEpiC	eye:	n/a
41	chr12:47221046-47221096	AG09309	skin:	n/a
42	chr12:47221046-47221096	K562	blood:	n/a
43	chr12:47221046-47221096	HCPEpiC	choroid plexus:	n/a
44	chr12:47221046-47221096	Jurkat	blood:	n/a
45	chr12:47221046-47221096	LNCaP	prostate:	n/a
46	chr12:47221046-47221096	ovcar-3	ovarian:	n/a
47	chr12:47221046-47221096	HCT-116	colon:	n/a
48	chr12:47221046-47221096	IMR90	lung:	fetal
49	chr12:47221046-47221096	NT2-D1	testis:	n/a
50	chr12:47221046-47221096	MCF10A-Er-Src	breast:	n/a

No data

Variant related genes	Relation type
SLC38A4	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10748455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10785645	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11183626	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465212	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465589	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2465592	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2465603	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2465631	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2715785	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4323984	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497488	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4516050	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4533116	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4569081	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4627160	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7955552	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7959916	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7974393	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47219800-47221800	Weak transcription	Esophagus	oesophagus
2	chr12:47219800-47224000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:47219800-47224200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:47219800-47224200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:47219800-47224400	Weak transcription	Right Ventricle	heart
6	chr12:47220000-47224600	Weak transcription	Pancreas	Pancrea
7	chr12:47220200-47221200	Enhancers	Liver	Liver
8	chr12:47220200-47221800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:47220200-47224000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:47220200-47224200	Weak transcription	NHEK	skin
11	chr12:47220200-47224400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:47220200-47224400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:47220600-47224200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:47220600-47224800	Weak transcription	HSMM	muscle
15	chr12:47221000-47221200	Enhancers	Pancreatic Islets	Pancreatic Islet

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