Variant report

Variant	rs58894799
Chromosome Location	chr5:126258482-126258483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 184 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10040840	0.82[EUR][1000 genomes]
rs10519919	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10519922	1.00[EUR][1000 genomes]
rs10519923	1.00[EUR][1000 genomes]
rs12518420	1.00[EUR][1000 genomes]
rs12651864	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12652390	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12652417	1.00[EUR][1000 genomes]
rs12653000	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12653290	1.00[EUR][1000 genomes]
rs12653444	1.00[EUR][1000 genomes]
rs12654717	1.00[EUR][1000 genomes]
rs12654725	1.00[EUR][1000 genomes]
rs12654808	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12655006	1.00[EUR][1000 genomes]
rs12655199	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12655223	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12655258	1.00[EUR][1000 genomes]
rs12655319	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655435	1.00[EUR][1000 genomes]
rs12655605	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12655726	1.00[EUR][1000 genomes]
rs12655928	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12655991	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656236	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12656537	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656837	1.00[EUR][1000 genomes]
rs12658138	1.00[EUR][1000 genomes]
rs12658174	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12658599	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658608	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12658816	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658821	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12658822	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12659476	1.00[EUR][1000 genomes]
rs12659607	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12659614	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12659633	1.00[EUR][1000 genomes]
rs17165192	1.00[EUR][1000 genomes]
rs17165194	1.00[EUR][1000 genomes]
rs17165211	1.00[EUR][1000 genomes]
rs17165228	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17165234	1.00[EUR][1000 genomes]
rs17165239	1.00[EUR][1000 genomes]
rs17165249	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34416835	1.00[EUR][1000 genomes]
rs34738240	1.00[EUR][1000 genomes]
rs35566904	1.00[EUR][1000 genomes]
rs35627668	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36091921	1.00[EUR][1000 genomes]
rs3812061	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141169	1.00[EUR][1000 genomes]
rs55792418	1.00[EUR][1000 genomes]
rs55802546	1.00[EUR][1000 genomes]
rs56094173	1.00[EUR][1000 genomes]
rs56122855	0.92[EUR][1000 genomes]
rs56124224	1.00[EUR][1000 genomes]
rs56272610	1.00[EUR][1000 genomes]
rs56688052	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56689722	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56786115	1.00[EUR][1000 genomes]
rs57031083	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57032367	1.00[EUR][1000 genomes]
rs57052202	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57081850	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57113926	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57485054	0.82[EUR][1000 genomes]
rs57627287	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57700815	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57833976	1.00[EUR][1000 genomes]
rs57906418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57915728	1.00[EUR][1000 genomes]
rs57985342	0.91[AFR][1000 genomes]
rs58164143	1.00[EUR][1000 genomes]
rs58249730	0.91[EUR][1000 genomes]
rs58262537	1.00[EUR][1000 genomes]
rs58527455	1.00[EUR][1000 genomes]
rs58646561	1.00[EUR][1000 genomes]
rs58838495	0.82[EUR][1000 genomes]
rs59459356	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59489123	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59643871	1.00[EUR][1000 genomes]
rs59676931	1.00[EUR][1000 genomes]
rs59814275	1.00[EUR][1000 genomes]
rs60045571	0.82[EUR][1000 genomes]
rs60068645	0.91[AFR][1000 genomes]
rs60138815	1.00[EUR][1000 genomes]
rs60244211	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60615137	1.00[EUR][1000 genomes]
rs60636815	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60781824	1.00[EUR][1000 genomes]
rs60889784	1.00[EUR][1000 genomes]
rs61031864	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61258380	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61279308	1.00[EUR][1000 genomes]
rs61463824	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61496590	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61647801	0.95[ASN][1000 genomes]
rs61653213	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61685918	1.00[EUR][1000 genomes]
rs6862462	1.00[EUR][1000 genomes]
rs6864607	0.82[EUR][1000 genomes]
rs6872893	1.00[EUR][1000 genomes]
rs6877692	1.00[EUR][1000 genomes]
rs6882025	1.00[EUR][1000 genomes]
rs6883181	1.00[EUR][1000 genomes]
rs6888532	1.00[EUR][1000 genomes]
rs6893763	1.00[EUR][1000 genomes]
rs6899030	1.00[EUR][1000 genomes]
rs72505648	0.82[EUR][1000 genomes]
rs73335426	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73335444	0.82[EUR][1000 genomes]
rs73335447	0.82[EUR][1000 genomes]
rs73335461	0.82[EUR][1000 genomes]
rs73335474	0.82[EUR][1000 genomes]
rs73335490	1.00[EUR][1000 genomes]
rs73335494	1.00[EUR][1000 genomes]
rs73335498	1.00[EUR][1000 genomes]
rs73335501	1.00[EUR][1000 genomes]
rs73337225	0.84[EUR][1000 genomes]
rs73337229	1.00[EUR][1000 genomes]
rs73337233	1.00[EUR][1000 genomes]
rs73337299	1.00[EUR][1000 genomes]
rs73783476	0.82[EUR][1000 genomes]
rs73783496	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73783501	1.00[EUR][1000 genomes]
rs73783503	1.00[EUR][1000 genomes]
rs73783504	1.00[EUR][1000 genomes]
rs73783506	1.00[EUR][1000 genomes]
rs73783507	1.00[EUR][1000 genomes]
rs73786207	1.00[EUR][1000 genomes]
rs73786209	1.00[EUR][1000 genomes]
rs73786212	1.00[EUR][1000 genomes]
rs73786239	1.00[EUR][1000 genomes]
rs73786240	1.00[EUR][1000 genomes]
rs73786241	1.00[EUR][1000 genomes]
rs73786242	1.00[EUR][1000 genomes]
rs73786244	1.00[EUR][1000 genomes]
rs73786246	1.00[EUR][1000 genomes]
rs73786247	1.00[EUR][1000 genomes]
rs73786249	1.00[EUR][1000 genomes]
rs73786250	1.00[EUR][1000 genomes]
rs73786251	1.00[EUR][1000 genomes]
rs73786252	1.00[EUR][1000 genomes]
rs73786253	1.00[EUR][1000 genomes]
rs73786255	1.00[EUR][1000 genomes]
rs73786259	1.00[EUR][1000 genomes]
rs73786260	1.00[EUR][1000 genomes]
rs73786261	1.00[EUR][1000 genomes]
rs73786262	1.00[EUR][1000 genomes]
rs73786264	1.00[EUR][1000 genomes]
rs73786265	1.00[EUR][1000 genomes]
rs73786266	1.00[EUR][1000 genomes]
rs73786267	0.92[EUR][1000 genomes]
rs73786268	1.00[EUR][1000 genomes]
rs73786269	1.00[EUR][1000 genomes]
rs73786270	1.00[EUR][1000 genomes]
rs73786271	1.00[EUR][1000 genomes]
rs73786272	1.00[EUR][1000 genomes]
rs73786276	1.00[EUR][1000 genomes]
rs73786277	1.00[EUR][1000 genomes]
rs73786278	1.00[EUR][1000 genomes]
rs73786280	1.00[EUR][1000 genomes]
rs73786281	1.00[EUR][1000 genomes]
rs73786282	1.00[EUR][1000 genomes]
rs73786283	1.00[EUR][1000 genomes]
rs73786284	1.00[EUR][1000 genomes]
rs73786285	1.00[EUR][1000 genomes]
rs73786287	1.00[EUR][1000 genomes]
rs73786288	1.00[EUR][1000 genomes]
rs73786290	1.00[EUR][1000 genomes]
rs73786294	1.00[EUR][1000 genomes]
rs73786295	1.00[EUR][1000 genomes]
rs73786298	1.00[EUR][1000 genomes]
rs73787403	1.00[EUR][1000 genomes]
rs73787404	1.00[EUR][1000 genomes]
rs73787406	1.00[EUR][1000 genomes]
rs7701976	0.82[EUR][1000 genomes]
rs7715377	0.82[EUR][1000 genomes]
rs7727719	0.82[EUR][1000 genomes]
rs9918233	1.00[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	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126244400-126261200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:126246200-126259800	Weak transcription	Fetal Kidney	kidney
3	chr5:126253600-126300400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:126254000-126261800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:126254000-126277800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:126254000-126278800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:126255400-126272400	Weak transcription	HSMM	muscle
8	chr5:126255600-126263200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:126255600-126272400	Weak transcription	HSMMtube	muscle
10	chr5:126256200-126259000	Weak transcription	Primary T cells from cord blood	blood
11	chr5:126256200-126261000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:126256400-126259400	Enhancers	Left Ventricle	heart
13	chr5:126257200-126262000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:126257200-126267800	Weak transcription	Psoas Muscle	Psoas
15	chr5:126257400-126260200	Weak transcription	Brain Anterior Caudate	brain
16	chr5:126257400-126261800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:126257400-126263200	Weak transcription	Brain Substantia Nigra	brain
18	chr5:126257600-126259200	Enhancers	K562	blood
19	chr5:126257800-126262800	Enhancers	Fetal Heart	heart
20	chr5:126257800-126267800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr5:126257800-126274000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:126258000-126259000	Weak transcription	Ovary	ovary
23	chr5:126258000-126259600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:126258000-126259800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:126258000-126260000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:126258000-126260600	Weak transcription	Brain Germinal Matrix	brain
27	chr5:126258000-126261400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:126258000-126261800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:126258000-126261800	Weak transcription	Right Atrium	heart
30	chr5:126258000-126262000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:126258000-126262000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:126258000-126262000	Weak transcription	Right Ventricle	heart
33	chr5:126258000-126263200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:126258000-126263200	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:126258000-126266600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:126258000-126266600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:126258000-126274800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:126258200-126261600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:126258200-126266600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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