Variant report

Variant	rs2720302
Chromosome Location	chr12:50179021-50179022
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	chr12:50177362..50179959-chr12:50184689..50186718,2	MCF-7	breast:
2	chr12:50178156..50180784-chr12:50182725..50184886,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11169162	0.82[AMR][1000 genomes]
rs11611070	0.83[EUR][1000 genomes]
rs11612227	0.81[EUR][1000 genomes]
rs11615911	0.81[AMR][1000 genomes]
rs2603105	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2603112	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2603116	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720287	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2720301	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075681	0.81[EUR][1000 genomes]
rs4488285	0.81[AMR][1000 genomes]
rs59046026	0.81[AMR][1000 genomes]
rs59766494	0.81[AMR][1000 genomes]
rs60062868	0.81[AMR][1000 genomes]
rs66721590	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66924167	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73114127	0.81[EUR][1000 genomes]
rs73114136	0.81[EUR][1000 genomes]
rs73114137	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73114141	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7313563	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs751675	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7953534	0.80[EUR][1000 genomes]
rs7977000	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7978693	0.82[EUR][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50158800-50181600	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:50160600-50183400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:50170000-50184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:50170200-50184400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:50170800-50191200	Weak transcription	Brain Substantia Nigra	brain
6	chr12:50172000-50183400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:50172400-50183800	Weak transcription	Pancreas	Pancrea
8	chr12:50172400-50192600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:50172800-50184600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:50176400-50179600	Enhancers	Fetal Muscle Trunk	muscle
12	chr12:50176600-50179600	Enhancers	HUVEC	blood vessel
13	chr12:50176800-50179200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:50177000-50179200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:50177000-50179200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:50177200-50179200	Enhancers	HSMMtube	muscle
17	chr12:50177200-50179600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:50177400-50183800	Weak transcription	Liver	Liver
19	chr12:50177600-50179200	Enhancers	Hela-S3	cervix
20	chr12:50177800-50183200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
22	chr12:50178200-50179400	Enhancers	A549	lung
23	chr12:50178200-50181400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:50178200-50181600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:50178200-50184400	Weak transcription	Aorta	Aorta
26	chr12:50178400-50181400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:50178400-50183400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:50178400-50184600	Weak transcription	Ovary	ovary
29	chr12:50178400-50194000	Weak transcription	NH-A	brain
30	chr12:50178400-50195000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:50178600-50181400	Weak transcription	Osteobl	bone
32	chr12:50178600-50181600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:50178600-50183400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:50178600-50183400	Weak transcription	Adipose Nuclei	Adipose
35	chr12:50178600-50183400	Weak transcription	Psoas Muscle	Psoas
36	chr12:50178600-50184400	Weak transcription	Spleen	Spleen
37	chr12:50178600-50185600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:50178800-50180800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:50178800-50181400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:50178800-50181400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:50178800-50181400	Weak transcription	HSMM	muscle
42	chr12:50178800-50181600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:50178800-50181600	Weak transcription	Fetal Lung	lung
44	chr12:50178800-50183200	Weak transcription	Placenta	Placenta
45	chr12:50178800-50183400	Weak transcription	Fetal Stomach	stomach
46	chr12:50178800-50183400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:50178800-50183400	Weak transcription	NHLF	lung
48	chr12:50178800-50183600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:50178800-50184400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:50178800-50184600	Weak transcription	Right Ventricle	heart

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