Variant report

Variant	rs12312294
Chromosome Location	chr12:120449985-120449986
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120448826..120451123-chr12:120516985..120519122,2	MCF-7	breast:
2	chr12:120426089..120427906-chr12:120449284..120451965,2	K562	blood:
3	chr12:120443342..120446063-chr12:120447694..120450232,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10161261	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10849733	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10849734	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11064985	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11064990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11064995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11064997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11065005	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11065010	0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11065019	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11065024	0.85[CEU][hapmap];1.00[GIH][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12298267	1.00[CEU][hapmap]
rs12307887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12313412	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12314638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12316670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12425507	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13377680	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59709506	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61748076	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7139151	0.85[CEU][hapmap]
rs7294975	0.82[CEU][hapmap]
rs7300507	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7307905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73410866	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73410877	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7953284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953368	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7957793	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7964192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964299	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7964301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970773	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970908	1.00[GIH][hapmap];0.84[LWK][hapmap]
rs7974285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr12:120428600-120453200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:120428800-120451400	Weak transcription	HMEC	breast
3	chr12:120428800-120451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:120429000-120450000	Weak transcription	Esophagus	oesophagus
5	chr12:120437800-120462400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:120438800-120451400	Weak transcription	A549	lung
7	chr12:120442200-120451400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:120444800-120451200	Weak transcription	Hela-S3	cervix
9	chr12:120444800-120451400	Weak transcription	NHEK	skin
10	chr12:120445400-120450000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:120445600-120451800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:120445600-120453200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:120446000-120451200	Weak transcription	HepG2	liver
14	chr12:120446000-120451600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:120447400-120454600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:120447600-120454200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:120447600-120454200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:120447800-120454200	Enhancers	Primary T cells from cord blood	blood
19	chr12:120448400-120454200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:120448400-120454200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:120448600-120454000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:120449000-120450000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:120449000-120450800	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr12:120449200-120450200	Weak transcription	Fetal Thymus	thymus
25	chr12:120449200-120451200	Weak transcription	Thymus	Thymus
26	chr12:120449200-120453000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:120449400-120450000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:120449400-120451000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:120449600-120450000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr12:120449600-120450000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:120449600-120450000	Enhancers	GM12878-XiMat	blood
32	chr12:120449600-120450200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr12:120449800-120450200	Active TSS	Brain Anterior Caudate	brain
34	chr12:120449800-120450400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:120449800-120450400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:120449800-120450400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr12:120449800-120450800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:120449800-120450800	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:120449800-120451400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links