Variant report

Variant	rs294494
Chromosome Location	chr5:58881670-58881671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10037874	0.93[ASN][1000 genomes]
rs1395336	0.95[MEX][hapmap]
rs159194	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs159196	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs159197	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs177077	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs294478	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294479	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294481	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs294482	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294483	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs294484	0.90[CHB][hapmap]
rs294485	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs294486	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294492	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs294496	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs294497	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs294498	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs294500	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295943	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs295944	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295950	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295952	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295953	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295954	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295955	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295956	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295959	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295961	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs295963	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295964	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295966	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs295967	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295968	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295970	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295973	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs295979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs295980	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs296406	0.86[CEU][hapmap]
rs298014	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298025	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298027	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298028	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298029	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298030	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298032	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298033	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs298034	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs298038	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298039	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298040	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298043	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298044	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298045	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298046	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs298049	0.91[ASN][1000 genomes]
rs298051	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs298052	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs37569	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs37571	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs37579	0.95[MEX][hapmap]
rs431381	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858964	0.95[MEX][hapmap]

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	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58859200-58883400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:58859400-58884000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58878400-58882600	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr5:58878800-58888200	Active TSS	Psoas Muscle	Psoas
5	chr5:58879000-58882800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:58879000-58882800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:58879000-58884200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr5:58879200-58883800	Active TSS	Fetal Brain Female	brain
9	chr5:58879200-58884800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr5:58879200-58885000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:58879400-58884000	Active TSS	Brain Substantia Nigra	brain
12	chr5:58879600-58882600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:58879600-58882600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:58879600-58883200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:58879600-58883800	Active TSS	Stomach Mucosa	stomach
16	chr5:58879600-58884200	Active TSS	Colonic Mucosa	Colon
17	chr5:58879600-58884400	Active TSS	Brain Angular Gyrus	brain
18	chr5:58879800-58883200	Weak transcription	Fetal Thymus	thymus
19	chr5:58879800-58883200	Weak transcription	Gastric	stomach
20	chr5:58879800-58883600	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr5:58880000-58881800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr5:58880000-58882200	Active TSS	Fetal Intestine Large	intestine
23	chr5:58880000-58882600	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:58880000-58882600	Weak transcription	Fetal Stomach	stomach
25	chr5:58880000-58883200	Weak transcription	Aorta	Aorta
26	chr5:58880000-58883200	Weak transcription	Liver	Liver
27	chr5:58880000-58884000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr5:58880000-58884000	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr5:58880000-58884400	Active TSS	Brain Cingulate Gyrus	brain
30	chr5:58880200-58882600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:58880200-58882600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:58880200-58883000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:58880400-58882600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:58880400-58882600	Weak transcription	Small Intestine	intestine
35	chr5:58880400-58882800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:58880400-58883400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:58880400-58883600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:58880400-58883600	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr5:58880400-58883800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:58880400-58883800	Active TSS	Fetal Kidney	kidney
41	chr5:58880400-58884000	Active TSS	Brain Anterior Caudate	brain
42	chr5:58880800-58882800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr5:58880800-58883200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:58881000-58883200	Active TSS	Fetal Brain Male	brain
45	chr5:58881200-58882400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:58881200-58883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:58881200-58883800	Active TSS	Brain Hippocampus Middle	brain
48	chr5:58881400-58882200	Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr5:58881400-58882400	Active TSS	Brain Germinal Matrix	brain
50	chr5:58881400-58882400	Weak transcription	Rectal Smooth Muscle	rectum

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