Variant report

Variant	rs12227600
Chromosome Location	chr12:43206476-43206477
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	chr12:43201576..43204035-chr12:43205412..43207540,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1009431	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11181692	1.00[EUR][1000 genomes]
rs11181693	1.00[EUR][1000 genomes]
rs11181694	0.98[EUR][1000 genomes]
rs11181695	0.98[EUR][1000 genomes]
rs11181696	0.98[EUR][1000 genomes]
rs1400811	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1400814	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1517666	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1517667	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1517670	0.91[EUR][1000 genomes]
rs1517671	0.91[EUR][1000 genomes]
rs1517672	0.91[EUR][1000 genomes]
rs1554248	0.91[EUR][1000 genomes]
rs1554249	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1554250	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1554251	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1554252	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1607249	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17091970	0.91[EUR][1000 genomes]
rs17092061	0.99[EUR][1000 genomes]
rs1878577	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1878579	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1878580	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2037238	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2056192	0.92[EUR][1000 genomes]
rs2056193	0.88[ASN][1000 genomes]
rs2056196	0.93[EUR][1000 genomes]
rs2138862	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252131	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2255231	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2255712	0.91[EUR][1000 genomes]
rs2255713	0.91[EUR][1000 genomes]
rs2407112	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2407113	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2459736	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2459738	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2459739	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2459740	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2459741	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2459742	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2459743	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2468321	0.91[EUR][1000 genomes]
rs2468322	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2468324	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2468325	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2468326	0.91[EUR][1000 genomes]
rs2468327	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678102	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678103	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678104	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2678105	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2678108	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2678109	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2678110	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2678111	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2678112	0.85[EUR][1000 genomes]
rs2678113	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2678117	0.88[ASN][1000 genomes]
rs2678119	0.89[ASN][1000 genomes]
rs2678132	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678134	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678135	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678136	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678137	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678141	0.93[EUR][1000 genomes]
rs2678143	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678144	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678145	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678146	0.91[EUR][1000 genomes]
rs2678147	0.91[EUR][1000 genomes]
rs2678148	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2678149	0.91[EUR][1000 genomes]
rs2678151	0.91[EUR][1000 genomes]
rs2678152	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2678153	0.91[EUR][1000 genomes]
rs2730965	0.91[EUR][1000 genomes]
rs2730966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2730967	0.91[EUR][1000 genomes]
rs2730968	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2730969	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2730970	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2730976	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2730977	0.91[EUR][1000 genomes]
rs2730980	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2730991	0.89[ASN][1000 genomes]
rs2730997	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2730998	0.91[EUR][1000 genomes]
rs2730999	0.91[EUR][1000 genomes]
rs2731000	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731002	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731003	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731004	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731010	0.85[EUR][1000 genomes]
rs2731015	0.85[EUR][1000 genomes]
rs2731016	0.85[EUR][1000 genomes]
rs2731017	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2956457	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35204519	0.85[EUR][1000 genomes]
rs73130905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314719	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7962735	1.00[EUR][1000 genomes]
rs7962980	0.81[EUR][1000 genomes]
rs7976494	1.00[EUR][1000 genomes]
rs7976690	1.00[EUR][1000 genomes]
rs908656	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908657	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908658	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908660	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908661	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908662	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908663	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs908666	0.98[EUR][1000 genomes]
rs952054	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs952056	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9651992	0.98[EUR][1000 genomes]
rs973001	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs975540	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9788178	1.00[EUR][1000 genomes]
rs981248	0.91[EUR][1000 genomes]
rs991703	0.80[AMR][1000 genomes];0.91[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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv558749	chr12:43180190-43275097	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43197200-43206800	Weak transcription	Psoas Muscle	Psoas
2	chr12:43201800-43207400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:43202200-43207600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:43202400-43207200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:43204000-43208800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:43204200-43209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:43205600-43206800	Enhancers	Fetal Heart	heart
8	chr12:43206400-43206600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:43206400-43207400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:43206400-43207400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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