Variant report

Variant	rs295960
Chromosome Location	chr5:58902841-58902842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10805516	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159194	0.88[ASN][1000 genomes]
rs159196	0.92[ASN][1000 genomes]
rs159197	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs177078	0.88[ASN][1000 genomes]
rs186078	0.87[ASN][1000 genomes]
rs190936	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294477	0.87[ASN][1000 genomes]
rs294478	0.88[ASN][1000 genomes]
rs294479	0.88[ASN][1000 genomes]
rs294481	0.88[ASN][1000 genomes]
rs294482	0.87[ASN][1000 genomes]
rs294483	0.88[ASN][1000 genomes]
rs294484	0.88[ASN][1000 genomes]
rs294485	0.86[ASN][1000 genomes]
rs294486	0.88[ASN][1000 genomes]
rs294492	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs294495	0.95[ASN][1000 genomes]
rs294496	0.95[ASN][1000 genomes]
rs294497	0.95[ASN][1000 genomes]
rs294498	0.92[ASN][1000 genomes]
rs294499	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs294500	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs294501	0.92[ASN][1000 genomes]
rs294502	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295943	0.93[EUR][1000 genomes]
rs295944	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295948	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295950	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295955	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295957	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295963	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295964	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295966	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295970	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295971	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295972	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295973	0.96[ASN][1000 genomes]
rs295974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295975	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295978	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295979	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs295980	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298014	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298016	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298017	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298032	0.80[ASN][1000 genomes]
rs298033	0.80[ASN][1000 genomes]
rs298034	0.86[ASN][1000 genomes]
rs298036	0.88[ASN][1000 genomes]
rs298038	0.87[ASN][1000 genomes]
rs298039	0.87[ASN][1000 genomes]
rs298040	0.89[ASN][1000 genomes]
rs298041	0.90[ASN][1000 genomes]
rs298043	0.89[ASN][1000 genomes]
rs298044	0.90[ASN][1000 genomes]
rs298045	0.90[ASN][1000 genomes]
rs298046	0.89[ASN][1000 genomes]
rs298047	0.90[ASN][1000 genomes]
rs298048	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs298051	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298052	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298053	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37569	0.87[ASN][1000 genomes]
rs37570	0.88[ASN][1000 genomes]
rs37571	0.88[ASN][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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv598256	chr5:58893286-58939840	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58894800-58903000	Weak transcription	Psoas Muscle	Psoas
2	chr5:58894800-58903400	Weak transcription	Fetal Kidney	kidney
3	chr5:58894800-58904800	Weak transcription	HSMMtube	muscle
4	chr5:58894800-58910800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:58894800-58910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:58895800-58911200	Weak transcription	Hela-S3	cervix
7	chr5:58897000-58903000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:58897200-58903000	Weak transcription	Brain Angular Gyrus	brain
9	chr5:58897600-58905800	Weak transcription	Stomach Mucosa	stomach
10	chr5:58897600-58915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:58901200-58904400	Enhancers	Fetal Brain Male	brain
12	chr5:58902200-58903600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr5:58902400-58903400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:58902400-58903800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:58902400-58903800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:58902400-58903800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:58902400-58903800	Enhancers	Colon Smooth Muscle	Colon
18	chr5:58902400-58903800	Enhancers	A549	lung
19	chr5:58902600-58903600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:58902600-58903600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr5:58902800-58903000	Enhancers	Fetal Brain Female	brain
22	chr5:58902800-58903000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr5:58902800-58903200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:58902800-58903200	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr5:58902800-58903200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr5:58902800-58903200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr5:58902800-58903200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:58902800-58903200	Enhancers	NHLF	lung
29	chr5:58902800-58903400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:58902800-58903400	Active TSS	Brain Hippocampus Middle	brain
31	chr5:58902800-58903400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:58902800-58903400	Active TSS	Brain Substantia Nigra	brain
33	chr5:58902800-58903600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr5:58902800-58903600	Flanking Active TSS	Fetal Lung	lung
35	chr5:58902800-58903800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:58902800-58903800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr5:58902800-58903800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr5:58902800-58903800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:58902800-58903800	Active TSS	Brain Anterior Caudate	brain

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