Variant report

Variant	rs71564854
Chromosome Location	chr6:56659460-56659461
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	chr6:56650785..56654475-chr6:56658761..56661696,4	MCF-7	breast:

Extended variants
information (count: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10498812	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10498813	0.93[EUR][1000 genomes]
rs11756551	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11970648	0.83[EUR][1000 genomes]
rs13190854	0.92[EUR][1000 genomes]
rs13192540	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13192931	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13194625	0.93[EUR][1000 genomes]
rs13194904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13195601	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13198204	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13198399	0.86[AMR][1000 genomes]
rs13198597	0.85[EUR][1000 genomes]
rs13200166	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13200559	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13200768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200868	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13201639	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13201733	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13203000	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13203148	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13203327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13203681	0.89[EUR][1000 genomes]
rs13204466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13205667	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13207768	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13208409	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13211879	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13214135	0.85[AMR][1000 genomes]
rs13214893	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13215883	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13217390	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13218913	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13219942	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13220618	0.93[EUR][1000 genomes]
rs13220628	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13220851	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1610156	0.80[EUR][1000 genomes]
rs1610157	0.88[EUR][1000 genomes]
rs16888171	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16888184	0.85[EUR][1000 genomes]
rs16888186	0.83[EUR][1000 genomes]
rs17684730	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17684748	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17684772	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17684784	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17684802	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17684878	0.89[EUR][1000 genomes]
rs17684884	0.89[EUR][1000 genomes]
rs17684941	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17751966	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17751977	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17752002	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17752046	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17752106	0.89[EUR][1000 genomes]
rs17752213	0.84[EUR][1000 genomes]
rs1903332	0.85[EUR][1000 genomes]
rs28360570	0.85[EUR][1000 genomes]
rs34083827	0.83[EUR][1000 genomes]
rs34171958	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34228698	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34359353	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34425815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34455199	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34465210	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34500949	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34520435	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34566275	0.93[AMR][1000 genomes]
rs34587484	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34612783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34614087	0.92[EUR][1000 genomes]
rs34623351	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34640766	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34803237	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34832779	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34866877	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34896026	0.92[EUR][1000 genomes]
rs34966024	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35073881	0.89[EUR][1000 genomes]
rs35080938	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35081015	0.93[EUR][1000 genomes]
rs35225175	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35242294	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35251663	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35326806	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs35407078	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35439100	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35440408	0.83[EUR][1000 genomes]
rs35440822	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35461301	0.92[EUR][1000 genomes]
rs35494794	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs35566812	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35609883	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35642890	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35696739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35828379	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35851452	0.92[EUR][1000 genomes]
rs35873865	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35876418	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35886823	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35986172	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36022925	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36037734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36094082	0.89[EUR][1000 genomes]
rs41267675	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4299824	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4348308	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4371846	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4415160	0.91[EUR][1000 genomes]
rs4457154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4532444	0.91[EUR][1000 genomes]
rs4587171	0.94[EUR][1000 genomes]
rs56037312	0.82[EUR][1000 genomes]
rs56368885	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58980183	0.93[EUR][1000 genomes]
rs59432342	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61601344	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62411366	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62411367	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62411372	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62411375	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62411376	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6904535	0.95[EUR][1000 genomes]
rs6905603	0.88[EUR][1000 genomes]
rs6910414	0.84[EUR][1000 genomes]
rs6914293	0.88[EUR][1000 genomes]
rs6918949	0.88[EUR][1000 genomes]
rs6928104	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6934714	0.91[EUR][1000 genomes]
rs71564855	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71564856	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564861	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564863	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7758867	0.91[EUR][1000 genomes]
rs7761501	0.89[EUR][1000 genomes]
rs7761729	0.88[EUR][1000 genomes]
rs7766565	0.83[EUR][1000 genomes]
rs7771085	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7775182	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1034418	chr6:56651245-56700449	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56650800-56659600	Weak transcription	Brain Germinal Matrix	brain
2	chr6:56651200-56660200	Weak transcription	HSMM	muscle
3	chr6:56654400-56662400	Enhancers	Brain Substantia Nigra	brain
4	chr6:56654600-56663000	Enhancers	Brain Hippocampus Middle	brain
5	chr6:56654600-56664400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr6:56655000-56660600	Weak transcription	NH-A	brain
7	chr6:56655200-56659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:56655400-56660600	Weak transcription	HUVEC	blood vessel
9	chr6:56655800-56667400	Weak transcription	Stomach Mucosa	stomach
10	chr6:56656000-56660600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:56657000-56661200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:56657800-56664400	Enhancers	HSMMtube	muscle
13	chr6:56658000-56659800	Enhancers	Colon Smooth Muscle	Colon
14	chr6:56658000-56661800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:56658200-56660000	Enhancers	A549	lung
16	chr6:56658200-56660600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:56658600-56659800	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:56658600-56660400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:56658600-56661000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr6:56658600-56664400	Enhancers	Fetal Heart	heart
21	chr6:56658800-56659600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:56658800-56659800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr6:56658800-56659800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr6:56658800-56659800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:56658800-56660000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:56658800-56660000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:56658800-56660000	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:56658800-56660000	Enhancers	HMEC	breast
29	chr6:56658800-56660800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:56658800-56661400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:56658800-56662400	Enhancers	H9 Cell Line	embryonic stem cell
32	chr6:56658800-56662400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:56658800-56662600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:56658800-56664600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:56659000-56659600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:56659000-56659600	Enhancers	NHEK	skin
37	chr6:56659000-56660000	Enhancers	Brain Angular Gyrus	brain
38	chr6:56659000-56660200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:56659000-56660800	Enhancers	Osteobl	bone
40	chr6:56659000-56661400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:56659000-56661600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:56659000-56663200	Enhancers	Brain Anterior Caudate	brain
43	chr6:56659000-56664200	Enhancers	NHDF-Ad	bronchial
44	chr6:56659200-56659600	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr6:56659200-56659600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:56659200-56659600	Enhancers	Ovary	ovary
47	chr6:56659200-56659600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr6:56659200-56659800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:56659200-56659800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:56659200-56659800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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