Variant report

Variant	rs12620667
Chromosome Location	chr2:54290997-54290998
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	chr2:54281996..54284399-chr2:54289462..54291009,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12623097	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1363060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1974771	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3929001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58851686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60191560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61740458	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7583626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585466	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12620667	RP11-477N3.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
2	chr2:54278800-54302400	Weak transcription	Left Ventricle	heart
3	chr2:54280000-54292400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:54280800-54291400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:54280800-54310000	Weak transcription	Ovary	ovary
6	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
7	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
9	chr2:54281000-54291200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54281200-54292400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:54282000-54291200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:54282200-54293800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:54283400-54291200	Weak transcription	Pancreas	Pancrea
15	chr2:54283400-54292400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:54285000-54291000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:54287200-54291200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:54287200-54291800	Weak transcription	HSMMtube	muscle
20	chr2:54287200-54293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
22	chr2:54287400-54295000	Weak transcription	K562	blood
23	chr2:54287600-54291400	Weak transcription	HSMM	muscle
24	chr2:54287600-54292600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54287800-54292400	Weak transcription	NH-A	brain
26	chr2:54288000-54291400	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:54288000-54291800	Weak transcription	Osteobl	bone
28	chr2:54288000-54292200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:54288000-54292200	Weak transcription	NHDF-Ad	bronchial
30	chr2:54288600-54292200	Enhancers	Fetal Brain Male	brain
31	chr2:54288800-54292200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
33	chr2:54290000-54293000	Enhancers	Brain Substantia Nigra	brain
34	chr2:54290200-54292600	Weak transcription	Brain Anterior Caudate	brain
35	chr2:54290600-54291200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:54290600-54291400	Enhancers	Stomach Mucosa	stomach
37	chr2:54290600-54291800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:54290600-54293200	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:54290600-54293600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:54290600-54293800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:54290600-54294400	Enhancers	HMEC	breast
42	chr2:54290800-54291000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:54290800-54291200	Enhancers	Stomach Smooth Muscle	stomach
44	chr2:54290800-54291400	Enhancers	Brain Angular Gyrus	brain
45	chr2:54290800-54291600	Enhancers	Primary B cells from peripheral blood	blood
46	chr2:54290800-54292000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr2:54290800-54292800	Enhancers	NHEK	skin

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