Variant report

Variant	rs59080342
Chromosome Location	chr17:60001047-60001048
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59998398..60002489-chr17:60141477..60145059,6	MCF-7	breast:
2	chr17:59988596..59990482-chr17:59998557..60001348,2	MCF-7	breast:
3	chr17:60000176..60003312-chr20:45769534..45773282,12	MCF-7	breast:
4	chr17:60000185..60003336-chr20:45770698..45773254,7	MCF-7	breast:
5	chr17:59999872..60002983-chr17:60003853..60006368,4	K562	blood:
6	chr17:60000286..60003395-chr20:45777062..45778970,10	MCF-7	breast:
7	chr17:60000293..60003347-chr17:60077585..60080426,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10512492	0.88[AMR][1000 genomes]
rs11079459	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12451910	0.86[AMR][1000 genomes]
rs12452094	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12452732	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12452742	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12600620	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12600909	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12604037	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16945692	0.85[AMR][1000 genomes]
rs16945753	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16945756	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16945759	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16945801	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2271576	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28654524	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3744434	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968408	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968451	0.83[AMR][1000 genomes]
rs4968452	0.84[AMR][1000 genomes]
rs4968454	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968455	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968456	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4968457	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968459	0.80[ASN][1000 genomes]
rs4968460	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968461	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968462	1.00[AFR][1000 genomes]
rs4968463	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4968464	0.96[AFR][1000 genomes]
rs4988344	0.84[AMR][1000 genomes]
rs56794817	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57137451	0.84[AFR][1000 genomes]
rs57746689	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58085921	0.86[ASN][1000 genomes]
rs58241345	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58624595	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60053512	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61169879	0.81[AMR][1000 genomes]
rs61658218	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7218724	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7221089	0.83[AMR][1000 genomes]
rs73332565	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73332580	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73332598	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73334621	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8065778	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8066964	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8074890	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8080599	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8081917	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630735	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9630736	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
3	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
4	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
5	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
6	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
9	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas
10	chr17:59975400-60004600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:59978600-60004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:59980200-60003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:59982600-60001400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:59982600-60003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:59983600-60004600	Weak transcription	Spleen	Spleen
16	chr17:59984200-60003400	Weak transcription	HSMMtube	muscle
17	chr17:59985000-60004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:59987800-60002600	Weak transcription	NHEK	skin
19	chr17:59989000-60001600	Weak transcription	Brain Germinal Matrix	brain
20	chr17:59989200-60001400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:59989200-60003400	Weak transcription	Colon Smooth Muscle	Colon
22	chr17:59989400-60001400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr17:59989400-60003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:59989400-60003800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr17:59989400-60004400	Weak transcription	Lung	lung
26	chr17:59989600-60003600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:59989600-60003600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr17:59989600-60003600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:59989600-60003800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:59989600-60003800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr17:59989600-60003800	Weak transcription	Right Ventricle	heart
32	chr17:59989600-60003800	Weak transcription	HUVEC	blood vessel
33	chr17:59989600-60003800	Weak transcription	K562	blood
34	chr17:59989600-60003800	Weak transcription	NHLF	lung
35	chr17:59991800-60002200	Weak transcription	Hela-S3	cervix
36	chr17:59992800-60002800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr17:59993800-60002800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:59994000-60002400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr17:59994000-60002800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr17:59994200-60002600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:59994200-60002600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr17:59994200-60002800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr17:59994400-60002600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:59994400-60003000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:59994400-60003200	Strong transcription	Fetal Muscle Leg	muscle
46	chr17:59994600-60002400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr17:59994800-60003600	Weak transcription	Fetal Brain Male	brain
48	chr17:59995000-60001400	Weak transcription	NH-A	brain
49	chr17:59995000-60002800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:59995600-60002800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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