Variant report

Variant	rs12485289
Chromosome Location	chr3:85017400-85017401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:85011548..85014009-chr3:85014905..85018347,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11127869	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12632010	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637056	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17022119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17022236	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022250	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022300	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17043532	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1872554	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2172846	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2200466	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2220245	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2326121	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55916509	0.89[ASN][1000 genomes]
rs62250601	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6789062	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72029051	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646952	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3365261	chr3:85016662-85021560	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85011600-85018400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr3:85013400-85019200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:85014400-85020000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:85016200-85017600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:85016200-85018000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:85016400-85017600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:85016600-85017600	Enhancers	Fetal Brain Male	brain
8	chr3:85016600-85017800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:85016600-85018000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:85016600-85018200	Active TSS	Psoas Muscle	Psoas
11	chr3:85016800-85017400	Active TSS	Brain Angular Gyrus	brain
12	chr3:85016800-85017600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr3:85016800-85017600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr3:85016800-85017600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:85016800-85017600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:85016800-85018000	Active TSS	Brain Hippocampus Middle	brain
17	chr3:85016800-85018000	Active TSS	Brain Substantia Nigra	brain
18	chr3:85016800-85018000	Enhancers	Fetal Lung	lung
19	chr3:85016800-85018000	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr3:85016800-85018200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:85016800-85018400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:85016800-85018400	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr3:85016800-85019200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:85017000-85017400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr3:85017000-85017400	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr3:85017000-85017600	Active TSS	Brain Anterior Caudate	brain
27	chr3:85017000-85017600	Active TSS	Brain Germinal Matrix	brain
28	chr3:85017000-85017600	Active TSS	Fetal Brain Female	brain
29	chr3:85017200-85017400	Active TSS	Brain Cingulate Gyrus	brain
30	chr3:85017200-85017800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:85017200-85018200	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:85017200-85018200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:85017400-85017600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr3:85017400-85017800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:85017400-85017800	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr3:85017400-85018000	Flanking Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links