Variant report

Variant	rs2522258
Chromosome Location	chr12:47377589-47377590
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47370674..47373663-chr12:47375762..47378000,3	K562	blood:
2	chr12:47337092..47338034-chr12:47377347..47378031,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10785649	0.87[EUR][1000 genomes]
rs10881023	0.87[EUR][1000 genomes]
rs10881025	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs11183695	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11183699	0.82[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11183711	0.81[EUR][1000 genomes]
rs1989912	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2263492	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408647	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2522263	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2522269	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2522275	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2522277	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2711695	0.87[EUR][1000 genomes]
rs2711699	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2711702	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4291756	0.82[ASN][1000 genomes]
rs4768769	0.87[EUR][1000 genomes]
rs7139072	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7305283	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7971310	0.83[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs7972871	0.83[EUR][1000 genomes]
rs7978006	0.87[EUR][1000 genomes]
rs7979771	0.87[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	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
2	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47376200-47378000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:47376400-47377800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:47376400-47377800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:47376400-47378400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:47376400-47378400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:47376600-47377800	Enhancers	Esophagus	oesophagus
7	chr12:47376600-47378400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:47376800-47377800	Enhancers	Right Ventricle	heart
9	chr12:47376800-47377800	Flanking Active TSS	NHEK	skin
10	chr12:47376800-47378200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:47376800-47378400	Enhancers	HMEC	breast
12	chr12:47377000-47377800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:47377000-47377800	Enhancers	Primary T cells from cord blood	blood
14	chr12:47377000-47377800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:47377000-47378000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:47377000-47378000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:47377000-47378200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr12:47377000-47379000	Enhancers	Hela-S3	cervix
19	chr12:47377200-47377800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:47377200-47377800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:47377200-47377800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr12:47377200-47377800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr12:47377200-47377800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:47377200-47377800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:47377200-47377800	Enhancers	Fetal Thymus	thymus
26	chr12:47377200-47377800	Enhancers	Left Ventricle	heart
27	chr12:47377200-47377800	Enhancers	HepG2	liver
28	chr12:47377200-47378000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:47377200-47378000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:47377200-47378000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:47377200-47378000	Enhancers	Fetal Heart	heart
32	chr12:47377200-47378200	Enhancers	Placenta	Placenta
33	chr12:47377200-47378400	Enhancers	Liver	Liver
34	chr12:47377200-47378600	Enhancers	HSMM	muscle
35	chr12:47377400-47377800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr12:47377400-47377800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:47377400-47378000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
38	chr12:47377400-47378000	Enhancers	Fetal Muscle Leg	muscle
39	chr12:47377400-47378400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links