Variant report

Variant	rs59790609
Chromosome Location	chr1:45087473-45087474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr1:45087370-45088113	IMR90	lung:	n/a	chr1:45087851-45087861
2	CEBPB	chr1:45087460-45087802	IMR90	lung:	n/a	n/a
3	BCL3	chr1:45087381-45087655	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45086965..45088510-chr1:45121277..45123002,2	MCF-7	breast:
2	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
3	chr1:45085649..45090231-chr1:45185338..45188930,8	K562	blood:

Variant related genes	Relation type
RNF220	TF binding region
ENSG00000199377	Chromatin interaction
ENSG00000198520	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1051664	0.94[ASN][1000 genomes]
rs1135319	1.00[EUR][1000 genomes]
rs56257701	0.93[ASN][1000 genomes]
rs58019041	0.93[ASN][1000 genomes]
rs58035624	0.88[ASN][1000 genomes]
rs58401148	0.93[ASN][1000 genomes]
rs58678671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59370761	0.93[ASN][1000 genomes]
rs59764933	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60469789	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60476008	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6429544	0.90[ASN][1000 genomes]
rs6665374	0.88[ASN][1000 genomes]
rs6667593	0.93[ASN][1000 genomes]
rs6698388	0.94[ASN][1000 genomes]
rs72671972	0.93[ASN][1000 genomes]
rs74070566	0.98[ASN][1000 genomes]
rs74070577	0.93[ASN][1000 genomes]
rs7539312	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45074800-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:45079600-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45082800-45087800	Enhancers	Brain Cingulate Gyrus	brain
4	chr1:45083000-45087600	Enhancers	Brain Hippocampus Middle	brain
5	chr1:45083000-45097000	Weak transcription	Spleen	Spleen
6	chr1:45083400-45089000	Enhancers	NHDF-Ad	bronchial
7	chr1:45083400-45097200	Weak transcription	Gastric	stomach
8	chr1:45083600-45097000	Weak transcription	Right Atrium	heart
9	chr1:45083800-45091200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:45083800-45096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:45083800-45096600	Weak transcription	Fetal Heart	heart
12	chr1:45084200-45097000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:45084800-45091000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:45084800-45096800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:45085600-45088200	Bivalent Enhancer	Fetal Kidney	kidney
16	chr1:45085600-45091000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:45085600-45097000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:45085600-45097000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:45085800-45090600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:45085800-45090800	Weak transcription	Fetal Brain Female	brain
21	chr1:45085800-45096600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:45085800-45096800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:45086000-45087600	Weak transcription	Fetal Lung	lung
24	chr1:45086000-45088400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:45086000-45091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:45086400-45089200	Weak transcription	K562	blood
27	chr1:45086400-45091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:45087000-45087600	Enhancers	Brain Substantia Nigra	brain
29	chr1:45087000-45088400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:45087000-45088600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:45087000-45088600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:45087000-45089000	Enhancers	NHLF	lung
33	chr1:45087200-45087600	Enhancers	Brain Angular Gyrus	brain
34	chr1:45087200-45087600	Enhancers	NH-A	brain
35	chr1:45087200-45087800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:45087200-45087800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:45087200-45087800	Enhancers	Brain Anterior Caudate	brain
38	chr1:45087200-45087800	Enhancers	HSMM	muscle
39	chr1:45087200-45088400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:45087200-45088600	Enhancers	Osteobl	bone
41	chr1:45087200-45096800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:45087400-45087600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:45087400-45087800	Enhancers	Brain Inferior Temporal Lobe	brain

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