Variant report

Variant	rs2138862
Chromosome Location	chr12:43183763-43183764
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	chr12:43173451..43175672-chr12:43183405..43185439,2	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	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11181692	0.93[EUR][1000 genomes]
rs11181693	0.93[EUR][1000 genomes]
rs11181694	0.91[EUR][1000 genomes]
rs11181695	0.91[EUR][1000 genomes]
rs11181696	0.91[EUR][1000 genomes]
rs12227600	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1400811	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1400814	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1517666	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1517667	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1517670	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1517671	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1517672	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1554248	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1554249	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1554250	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1554251	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1554252	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1607249	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17091970	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17092061	0.92[EUR][1000 genomes]
rs1878577	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1878579	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1878580	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2037238	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2056192	0.95[EUR][1000 genomes]
rs2056193	0.95[ASN][1000 genomes]
rs2056196	0.96[EUR][1000 genomes]
rs2252129	0.85[EUR][1000 genomes]
rs2252131	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2255231	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2255712	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2255713	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2407112	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2407113	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2459736	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2459738	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2459739	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2459740	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2459741	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2459742	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2459743	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468321	0.98[EUR][1000 genomes]
rs2468322	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2468324	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2468325	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2468326	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2468327	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678102	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678103	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678104	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2678105	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2678108	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2678109	0.93[EUR][1000 genomes]
rs2678110	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678111	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678112	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678113	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678117	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2678119	0.96[ASN][1000 genomes]
rs2678132	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678134	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678135	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678136	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678137	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678141	0.96[EUR][1000 genomes]
rs2678143	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678144	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678145	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678146	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678147	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678148	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2678149	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678151	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2678152	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2678153	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730965	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730966	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730967	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730968	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730969	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730970	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730976	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2730977	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730980	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2730991	0.96[ASN][1000 genomes]
rs2730997	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730998	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2730999	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731002	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731003	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731004	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731010	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731015	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731016	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731017	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2956457	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35204519	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73130905	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314719	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7962735	0.93[EUR][1000 genomes]
rs7976494	0.93[EUR][1000 genomes]
rs7976690	0.93[EUR][1000 genomes]
rs908656	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908657	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908658	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908660	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908661	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908662	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908663	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs908666	0.91[EUR][1000 genomes]
rs952054	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs952056	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9651992	0.91[EUR][1000 genomes]
rs973001	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs975540	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788178	0.93[EUR][1000 genomes]
rs981248	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs991703	0.84[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	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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43175000-43183800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:43175400-43184200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:43179400-43185800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:43180800-43184000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:43180800-43184400	Enhancers	Fetal Heart	heart
6	chr12:43181000-43183800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:43181000-43184000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:43181000-43184000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:43181000-43184000	Weak transcription	Osteobl	bone
10	chr12:43181000-43184800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:43181200-43184000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:43181200-43184000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:43181200-43184000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:43181200-43184000	Weak transcription	NH-A	brain
15	chr12:43181200-43185000	Weak transcription	Placenta	Placenta
16	chr12:43181400-43184400	Weak transcription	HSMMtube	muscle
17	chr12:43181600-43183800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:43181600-43184000	Weak transcription	HSMM	muscle
19	chr12:43181600-43184200	Weak transcription	NHLF	lung
20	chr12:43182200-43184000	Weak transcription	Fetal Lung	lung
21	chr12:43182800-43185400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:43183000-43184200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:43183200-43184000	Enhancers	HUVEC	blood vessel
24	chr12:43183200-43184400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:43183400-43184800	Enhancers	Left Ventricle	heart
26	chr12:43183400-43185000	Enhancers	Right Atrium	heart
27	chr12:43183400-43185400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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