Variant report

Variant	rs58142139
Chromosome Location	chr1:92730554-92730555
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	chr1:92724491..92726278-chr1:92728631..92730987,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10399671	0.87[EUR][1000 genomes]
rs11164423	0.83[AMR][1000 genomes]
rs11166542	0.88[AMR][1000 genomes]
rs12070923	0.83[AMR][1000 genomes]
rs12075168	0.87[EUR][1000 genomes]
rs12075243	0.87[EUR][1000 genomes]
rs12078746	0.88[AMR][1000 genomes]
rs12090761	0.83[AMR][1000 genomes]
rs12098095	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12142556	0.88[AFR][1000 genomes]
rs17131621	0.88[AMR][1000 genomes]
rs17131632	0.87[EUR][1000 genomes]
rs17131636	0.87[EUR][1000 genomes]
rs41286805	1.00[EUR][1000 genomes]
rs41296171	1.00[EUR][1000 genomes]
rs41313389	1.00[EUR][1000 genomes]
rs55993081	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56297403	1.00[EUR][1000 genomes]
rs56665661	0.83[AMR][1000 genomes]
rs57177520	1.00[EUR][1000 genomes]
rs57217458	1.00[EUR][1000 genomes]
rs57992264	0.88[AMR][1000 genomes]
rs58820626	0.86[AMR][1000 genomes]
rs59278612	1.00[EUR][1000 genomes]
rs60265386	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60550001	1.00[EUR][1000 genomes]
rs60755573	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60933677	1.00[EUR][1000 genomes]
rs61141829	1.00[EUR][1000 genomes]
rs61185080	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61410146	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6603970	0.83[AMR][1000 genomes]
rs6660858	1.00[EUR][1000 genomes]
rs6661028	1.00[EUR][1000 genomes]
rs6662565	0.88[AMR][1000 genomes]
rs6671543	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6672838	0.87[EUR][1000 genomes]
rs6679259	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6681027	0.88[AMR][1000 genomes]
rs6681213	1.00[EUR][1000 genomes]
rs6683456	0.87[EUR][1000 genomes]
rs6694248	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6695475	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702975	1.00[EUR][1000 genomes]
rs6704484	1.00[EUR][1000 genomes]
rs72958740	1.00[EUR][1000 genomes]
rs72958746	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958774	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958781	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958796	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960815	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960831	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960835	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960847	1.00[EUR][1000 genomes]
rs72960860	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960870	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960872	0.87[EUR][1000 genomes]
rs72962640	1.00[EUR][1000 genomes]
rs72962659	0.87[EUR][1000 genomes]
rs74101123	1.00[EUR][1000 genomes]
rs74101131	1.00[EUR][1000 genomes]
rs74101133	1.00[EUR][1000 genomes]
rs74101146	1.00[EUR][1000 genomes]
rs74101152	1.00[EUR][1000 genomes]
rs74101157	1.00[EUR][1000 genomes]
rs74102832	1.00[EUR][1000 genomes]
rs74102844	1.00[EUR][1000 genomes]
rs74102853	1.00[EUR][1000 genomes]
rs74102861	1.00[EUR][1000 genomes]
rs7513631	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519603	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7520555	1.00[EUR][1000 genomes]
rs7520675	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7525174	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527960	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7529971	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534750	1.00[EUR][1000 genomes]
rs7535181	0.88[AMR][1000 genomes]
rs7542362	1.00[EUR][1000 genomes]
rs7542736	0.87[EUR][1000 genomes]
rs7546528	0.83[AMR][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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv1794222	chr1:92711407-92735359	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92708200-92741200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:92709000-92737200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:92709400-92735800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:92709600-92730800	Weak transcription	Hela-S3	cervix
7	chr1:92710000-92737600	Weak transcription	HSMM	muscle
8	chr1:92710000-92745200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:92710200-92739400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:92710600-92753200	Weak transcription	Small Intestine	intestine
11	chr1:92710600-92762000	Weak transcription	Fetal Brain Male	brain
12	chr1:92710600-92763400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:92710600-92764000	Weak transcription	Gastric	stomach
14	chr1:92711000-92763600	Weak transcription	HSMMtube	muscle
15	chr1:92711200-92738200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:92711200-92742800	Weak transcription	NHLF	lung
17	chr1:92711200-92761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:92711200-92764000	Weak transcription	Spleen	Spleen
19	chr1:92715000-92731600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:92715600-92738200	Weak transcription	K562	blood
21	chr1:92717400-92734800	Weak transcription	Psoas Muscle	Psoas
22	chr1:92718000-92738200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:92719400-92745000	Weak transcription	Esophagus	oesophagus
24	chr1:92719400-92764000	Weak transcription	Pancreas	Pancrea
25	chr1:92719600-92730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:92719600-92760800	Weak transcription	Fetal Heart	heart
27	chr1:92720000-92763800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:92720200-92734400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:92720200-92737600	Weak transcription	Brain Anterior Caudate	brain
30	chr1:92720200-92739000	Weak transcription	Aorta	Aorta
31	chr1:92720400-92748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:92721400-92731400	Weak transcription	Fetal Kidney	kidney
33	chr1:92721600-92742400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:92722400-92763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:92723000-92763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:92724000-92731000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:92724000-92760600	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:92724200-92731400	Strong transcription	Fetal Thymus	thymus
39	chr1:92724200-92740800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:92724200-92745000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:92724200-92746200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:92724200-92746400	Strong transcription	Dnd41	blood
43	chr1:92724400-92736000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:92724400-92740000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:92724400-92746400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:92724400-92746600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:92724600-92763800	Weak transcription	Brain Substantia Nigra	brain
48	chr1:92724800-92747400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:92725200-92734800	Weak transcription	Brain Germinal Matrix	brain
50	chr1:92725400-92731400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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