Variant report

Variant	rs1059309
Chromosome Location	chr7:56061835-56061836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56060305..56063042-chr7:56167719..56169963,2	K562	blood:

Variant related genes	Relation type
ENSG00000238673	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10265826	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10274148	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1078650	0.91[ASN][1000 genomes]
rs1136390	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11974040	0.96[ASN][1000 genomes]
rs12154231	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12154781	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12155441	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12532776	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12668504	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12668532	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12669185	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12674147	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12674334	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13231257	0.93[ASN][1000 genomes]
rs2006649	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331095	0.90[ASN][1000 genomes]
rs28438587	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34795560	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34869068	0.90[ASN][1000 genomes]
rs35791463	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55852201	0.87[ASN][1000 genomes]
rs55940597	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58006921	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58981281	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59199266	0.82[ASN][1000 genomes]
rs59723101	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59849749	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60160896	0.93[ASN][1000 genomes]
rs60962915	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6593291	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6947853	0.83[ASN][1000 genomes]
rs6955639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970842	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6975697	0.90[ASN][1000 genomes]
rs73134780	0.90[ASN][1000 genomes]
rs73138774	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73138777	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73140793	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73140794	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7456530	0.93[ASN][1000 genomes]
rs7778601	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7781165	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7793536	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7795095	0.86[ASN][1000 genomes]
rs7798243	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7804578	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats 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	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1017793	chr7:56051267-56098030	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1059309	ZNF713	cis	parietal	SCAN
rs1059309	SUMF2	cis	Esophagus Muscularis	GTEx
rs1059309	SUMF2	cis	lymphoblastoid	seeQTL
rs1059309	SUMF2	cis	cerebellum	SCAN
rs1059309	SUMF2	cis	multi-tissue	Pritchard
rs1059309	SUMF2	cis	parietal	SCAN
rs1059309	SUMF2	cis	Liver	GTEx
rs1059309	ZNF713	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:56033800-56063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:56039200-56081600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:56039400-56062400	Weak transcription	Stomach Mucosa	stomach
6	chr7:56045000-56067400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:56045200-56068200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:56045400-56067000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr7:56045400-56067000	Strong transcription	Liver	Liver
10	chr7:56045400-56067200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr7:56045400-56067400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:56045600-56062400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:56045600-56066600	Strong transcription	Fetal Stomach	stomach
14	chr7:56045600-56067400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:56045600-56067400	Strong transcription	Fetal Intestine Large	intestine
16	chr7:56045800-56066800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:56045800-56068000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr7:56046200-56067200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:56046400-56065800	Strong transcription	Fetal Muscle Leg	muscle
20	chr7:56046400-56068200	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:56047000-56068400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:56048600-56062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:56048800-56062600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:56048800-56062600	Weak transcription	Gastric	stomach
25	chr7:56048800-56062600	Weak transcription	Spleen	Spleen
26	chr7:56048800-56062800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:56049000-56062400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:56049000-56062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:56049000-56062800	Weak transcription	Esophagus	oesophagus
30	chr7:56049200-56067000	Weak transcription	Fetal Heart	heart
31	chr7:56049200-56101600	Weak transcription	Small Intestine	intestine
32	chr7:56049400-56062800	Weak transcription	NHLF	lung
33	chr7:56049600-56062600	Weak transcription	A549	lung
34	chr7:56049800-56066400	Weak transcription	K562	blood
35	chr7:56050000-56086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr7:56051000-56062800	Weak transcription	Aorta	Aorta
37	chr7:56051400-56086800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:56051600-56062800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr7:56051600-56062800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:56051600-56062800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:56051600-56063000	Weak transcription	HMEC	breast
42	chr7:56051600-56064000	Weak transcription	HepG2	liver
43	chr7:56051800-56077000	Weak transcription	NHEK	skin
44	chr7:56052000-56062800	Weak transcription	Brain Angular Gyrus	brain
45	chr7:56052200-56062600	Weak transcription	Psoas Muscle	Psoas
46	chr7:56052800-56062600	Weak transcription	NHDF-Ad	bronchial
47	chr7:56052800-56064200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:56053000-56074200	Weak transcription	Hela-S3	cervix
49	chr7:56053000-56078200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:56053200-56062600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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