Variant report

Variant	rs10880806
Chromosome Location	chr12:45911861-45911862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45901440..45904259-chr12:45910126..45912673,2	MCF-7	breast:
2	chr12:45911413..45913925-chr12:46121246..46124442,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction
ENSG00000273015	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10736027	0.82[ASN][1000 genomes]
rs10785575	0.82[ASN][1000 genomes]
rs10785576	0.92[ASN][1000 genomes]
rs10785578	0.97[ASN][1000 genomes]
rs10880791	0.82[ASN][1000 genomes]
rs10880794	0.90[ASN][1000 genomes]
rs10880798	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880800	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10880803	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880804	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880805	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880807	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183067	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183068	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183069	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183072	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183077	0.93[ASN][1000 genomes]
rs11183078	0.93[ASN][1000 genomes]
rs11183079	0.93[ASN][1000 genomes]
rs12297127	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12298570	0.93[ASN][1000 genomes]
rs12303053	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12303449	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316574	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12317115	0.93[ASN][1000 genomes]
rs12320604	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12321802	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830362	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17096009	0.84[ASN][1000 genomes]
rs2408255	0.83[ASN][1000 genomes]
rs2408272	0.90[ASN][1000 genomes]
rs2408318	0.90[ASN][1000 genomes]
rs2408323	0.90[ASN][1000 genomes]
rs2897905	0.84[ASN][1000 genomes]
rs33971594	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34265125	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34865395	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35296382	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4567534	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4570651	0.90[ASN][1000 genomes]
rs4590938	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768090	0.92[ASN][1000 genomes]
rs4768091	0.91[ASN][1000 genomes]
rs4768623	0.90[ASN][1000 genomes]
rs5001653	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5003954	0.84[ASN][1000 genomes]
rs56217910	0.84[ASN][1000 genomes]
rs7133173	0.87[ASN][1000 genomes]
rs73285289	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7486952	0.82[ASN][1000 genomes]
rs7968560	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832395	chr12:45841765-46039297	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv508672	chr12:45884730-45931091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1791767	chr12:45892993-45912862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv691	chr12:45896295-45946455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv511498	chr12:45901586-45912862	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv558760	chr12:45901586-45913177	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv558761	chr12:45901586-45924964	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1792250	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1796155	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1803091	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1803348	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1807521	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1808857	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1814107	chr12:45903118-45912862	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv1828597	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1830594	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1834808	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv1836843	chr12:45903118-45912862	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv1842350	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv1842210	chr12:45903118-45940761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv1802574	chr12:45903265-45912862	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv558766	chr12:45903265-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv558767	chr12:45903265-45913177	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv558776	chr12:45903913-45913177	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 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	chr12:45910600-45912600	Enhancers	Thymus	Thymus
2	chr12:45910600-45913800	Enhancers	Fetal Thymus	thymus
3	chr12:45910800-45912200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:45911000-45913000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr12:45911400-45912000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:45911400-45913000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:45911800-45913000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:45911800-45913000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:45911800-45913200	Enhancers	Primary T cells from cord blood	blood
10	chr12:45911800-45913200	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links