Variant report

Variant	rs62344979
Chromosome Location	chr5:14343652-14343653
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14342477..14345158-chr5:14346178..14348281,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10866506	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10866507	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11133785	0.85[EUR][1000 genomes]
rs11949756	0.89[EUR][1000 genomes]
rs11950000	0.89[EUR][1000 genomes]
rs11959397	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109453	0.89[EUR][1000 genomes]
rs12109756	0.89[EUR][1000 genomes]
rs12109880	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12110161	0.89[EUR][1000 genomes]
rs12110267	1.00[EUR][1000 genomes]
rs16903421	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903423	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903428	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903434	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16903453	0.89[EUR][1000 genomes]
rs16903460	0.89[EUR][1000 genomes]
rs16903464	0.89[EUR][1000 genomes]
rs35373258	0.89[EUR][1000 genomes]
rs56689214	0.89[EUR][1000 genomes]
rs57017859	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57640930	0.89[EUR][1000 genomes]
rs59405120	0.91[EUR][1000 genomes]
rs60738268	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60768136	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60892841	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61059406	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61469842	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62344976	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62344981	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62344983	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62344984	0.88[EUR][1000 genomes]
rs62345009	0.95[EUR][1000 genomes]
rs62345012	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62345015	0.89[EUR][1000 genomes]
rs66554336	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs730185	0.88[EUR][1000 genomes]
rs73061636	0.89[EUR][1000 genomes]
rs7706484	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7710935	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7715916	0.89[EUR][1000 genomes]
rs7731443	0.84[AMR][1000 genomes];0.85[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	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14310600-14344600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:14319200-14349400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:14326800-14346400	Weak transcription	Fetal Kidney	kidney
4	chr5:14328000-14344400	Strong transcription	HMEC	breast
5	chr5:14330600-14344600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr5:14330600-14345000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:14331000-14348000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:14331400-14350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:14332600-14344400	Strong transcription	NHEK	skin
10	chr5:14334000-14349400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:14335000-14360600	Weak transcription	Psoas Muscle	Psoas
12	chr5:14335200-14348600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:14336400-14349400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:14337800-14346600	Weak transcription	Fetal Heart	heart
15	chr5:14338000-14357200	Weak transcription	Colonic Mucosa	Colon
16	chr5:14338400-14358000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:14338600-14348000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:14338800-14347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:14338800-14357600	Weak transcription	Esophagus	oesophagus
20	chr5:14339000-14343800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:14339000-14346400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:14339200-14344000	Weak transcription	Fetal Lung	lung
23	chr5:14339200-14357600	Weak transcription	Gastric	stomach
24	chr5:14339200-14358000	Weak transcription	Thymus	Thymus
25	chr5:14339200-14358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:14339400-14358400	Weak transcription	Fetal Thymus	thymus
27	chr5:14339800-14348800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:14340000-14347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:14340400-14353800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr5:14340600-14344000	Enhancers	Liver	Liver
31	chr5:14340800-14353600	Strong transcription	HSMM	muscle
32	chr5:14341000-14343800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:14341200-14350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:14341400-14344000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr5:14341400-14344200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr5:14341400-14355000	Weak transcription	Ovary	ovary
37	chr5:14341400-14359400	Weak transcription	Primary T cells from cord blood	blood
38	chr5:14341600-14347400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:14341600-14348600	Weak transcription	Aorta	Aorta
40	chr5:14341600-14357400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:14342000-14344200	Strong transcription	A549	lung
42	chr5:14342200-14343800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr5:14342400-14344200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:14342400-14347600	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:14342600-14344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:14342600-14344600	Weak transcription	Placenta	Placenta
47	chr5:14342600-14346200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:14342600-14346400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:14342600-14346400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:14342600-14357200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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