Variant report

Variant	rs12066340
Chromosome Location	chr1:210056359-210056360
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	chr1:210051709..210053987-chr1:210055689..210058098,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes]
rs10779514	1.00[AFR][1000 genomes]
rs10779515	1.00[AFR][1000 genomes]
rs10863789	1.00[AFR][1000 genomes]
rs10863790	1.00[AFR][1000 genomes]
rs1109430	1.00[AFR][1000 genomes]
rs11119347	1.00[AFR][1000 genomes]
rs11119348	1.00[AFR][1000 genomes]
rs11119359	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119360	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12058100	1.00[AFR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12063989	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12064085	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12064211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12064398	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes]
rs12078157	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12081405	1.00[AFR][1000 genomes]
rs12405750	1.00[AFR][1000 genomes]
rs12561766	1.00[AFR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12566152	1.00[AFR][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015255	1.00[AFR][1000 genomes]
rs17015268	1.00[AFR][1000 genomes]
rs1856161	1.00[AFR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038053	1.00[AFR][1000 genomes]
rs2064163	0.80[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes]
rs2235371	1.00[AFR][1000 genomes]
rs2235377	1.00[AFR][1000 genomes]
rs2272866	1.00[AFR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes]
rs3753517	1.00[AFR][1000 genomes]
rs41274836	1.00[AFR][1000 genomes]
rs4329516	1.00[AFR][1000 genomes]
rs4844491	1.00[AFR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes]
rs4844496	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4844498	0.96[AMR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57283682	1.00[AFR][1000 genomes]
rs9919217	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210049400-210056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:210051000-210057400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:210053000-210056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:210053400-210056400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:210053600-210057800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:210053600-210058000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:210053600-210058800	Enhancers	Brain Hippocampus Middle	brain
8	chr1:210053800-210056400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:210053800-210056400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:210053800-210056400	Weak transcription	HMEC	breast
11	chr1:210053800-210056800	Weak transcription	Hela-S3	cervix
12	chr1:210054000-210056400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:210054000-210056400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:210054000-210056600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:210055400-210056600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:210055600-210056400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:210055600-210060400	Enhancers	HSMMtube	muscle
18	chr1:210055800-210057800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:210055800-210058400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:210055800-210058400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:210055800-210060000	Weak transcription	Pancreas	Pancrea
22	chr1:210055800-210060200	Enhancers	HSMM	muscle
23	chr1:210056000-210056400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:210056000-210056400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:210056000-210057400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:210056200-210057000	Enhancers	NHDF-Ad	bronchial
27	chr1:210056200-210057200	Enhancers	NH-A	brain
28	chr1:210056200-210057200	Enhancers	Osteobl	bone
29	chr1:210056200-210058400	Enhancers	Fetal Brain Female	brain
30	chr1:210056200-210058600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:210056200-210060400	Enhancers	NHEK	skin

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