Variant report

Variant	rs17369708
Chromosome Location	chr5:59063333-59063334
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99093900..99094504-chr5:59063199..59063729,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000225850	Chromatin interaction
ENSG00000181274	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10043265	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10043283	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs10514857	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs11949859	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152908	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12187752	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs12188131	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13155799	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs1362941	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1362942	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437124	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs1504982	0.93[ASN][1000 genomes]
rs1504984	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16877195	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17310599	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17381667	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17381695	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17381723	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17382202	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17440909	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17441217	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17441825	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17742120	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17742544	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17743216	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17799161	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164660	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28583502	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4577665	0.93[ASN][1000 genomes]
rs4699942	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs4699943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700340	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700341	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs55704150	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55868825	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56199003	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56312915	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6450528	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs6450530	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs6860907	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs6874708	0.89[ASN][1000 genomes]
rs6889294	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs6897073	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751211	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72751218	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72751226	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72751229	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751231	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751232	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751233	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751234	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751235	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751237	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751241	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751244	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751247	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751250	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751252	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72751264	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751266	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs756211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703963	1.00[JPT][hapmap]
rs7708952	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs7710199	0.89[ASN][1000 genomes]
rs7736817	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs877745	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs981230	0.83[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59048800-59064000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:59052600-59064200	Weak transcription	Aorta	Aorta
3	chr5:59055800-59063600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:59060800-59065200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr5:59061400-59064400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:59061400-59065200	Active TSS	Fetal Brain Female	brain
7	chr5:59061600-59063400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:59061600-59065000	Active TSS	Colon Smooth Muscle	Colon
9	chr5:59061600-59065200	Active TSS	Rectal Smooth Muscle	rectum
10	chr5:59061600-59065200	Active TSS	A549	lung
11	chr5:59061800-59063800	Active TSS	Brain Germinal Matrix	brain
12	chr5:59061800-59065600	Active TSS	Hela-S3	cervix
13	chr5:59062000-59063400	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr5:59062000-59063800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:59062000-59063800	Flanking Active TSS	NHEK	skin
16	chr5:59062000-59064800	Active TSS	Fetal Stomach	stomach
17	chr5:59062000-59065200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr5:59062000-59065400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr5:59062200-59063600	Enhancers	Fetal Heart	heart
20	chr5:59062200-59064000	Active TSS	Brain Anterior Caudate	brain
21	chr5:59062200-59064000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr5:59062200-59064000	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr5:59062200-59065000	Active TSS	Colonic Mucosa	Colon
24	chr5:59062200-59065000	Active TSS	Fetal Kidney	kidney
25	chr5:59062200-59065200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:59062200-59065200	Active TSS	Right Atrium	heart
27	chr5:59062400-59063400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr5:59062400-59063600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:59062400-59065000	Active TSS	Fetal Muscle Trunk	muscle
30	chr5:59062600-59063400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr5:59062600-59063400	Weak transcription	Right Ventricle	heart
32	chr5:59062600-59063600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr5:59062600-59063600	Weak transcription	Esophagus	oesophagus
34	chr5:59062600-59063600	Weak transcription	Gastric	stomach
35	chr5:59062600-59063800	Active TSS	Primary B cells from peripheral blood	blood
36	chr5:59062600-59063800	Enhancers	Brain Cingulate Gyrus	brain
37	chr5:59062600-59063800	Weak transcription	Pancreas	Pancrea
38	chr5:59062600-59063800	Active TSS	Psoas Muscle	Psoas
39	chr5:59062600-59063800	Weak transcription	Spleen	Spleen
40	chr5:59062600-59064000	Active TSS	Stomach Smooth Muscle	stomach
41	chr5:59062600-59064200	Active TSS	Fetal Muscle Leg	muscle
42	chr5:59062600-59065000	Active TSS	Duodenum Mucosa	Duodenum
43	chr5:59062800-59063400	Weak transcription	Fetal Intestine Large	intestine
44	chr5:59062800-59063600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr5:59062800-59063800	Active TSS	Fetal Lung	lung
46	chr5:59062800-59064000	Weak transcription	HepG2	liver
47	chr5:59063000-59063400	Weak transcription	HSMM	muscle
48	chr5:59063000-59063600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:59063000-59063600	Enhancers	Liver	Liver
50	chr5:59063000-59063600	Active TSS	Fetal Brain Male	brain

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