Variant report

Variant	rs59066458
Chromosome Location	chr19:56137742-56137743
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	RUNX3	chr19:56137641-56138178	GM12878	blood:	n/a	chr19:56137914-56137923 chr19:56137914-56137931 chr19:56137914-56137923
2	NFIC	chr19:56137646-56138131	GM12878	blood:	n/a	n/a
3	BATF	chr19:56137731-56138094	GM12878	blood:	n/a	n/a
4	RUNX3	chr19:56137521-56138197	GM12878	blood:	n/a	chr19:56137914-56137923 chr19:56137914-56137931 chr19:56137914-56137923
5	BATF	chr19:56137686-56138070	GM12878	blood:	n/a	n/a
6	MTA3	chr19:56137621-56138159	GM12878	blood:	n/a	n/a
7	EP300	chr19:56137739-56137977	GM12878	blood:	n/a	n/a
8	ATF2	chr19:56137640-56138128	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56134500..56138557-chr19:56151822..56155582,4	K562	blood:
2	chr19:56110415..56112373-chr19:56134518..56138349,4	MCF-7	breast:
3	chr19:56109378..56114662-chr19:56134412..56139001,15	K562	blood:
4	chr19:56137436..56140208-chr19:56143830..56146164,3	MCF-7	breast:
5	chr19:56137710..56141334-chr19:56143393..56147099,4	K562	blood:
6	chr19:55918880..55921412-chr19:56134337..56137770,3	MCF-7	breast:
7	chr19:56134111..56136553-chr19:56137529..56140208,2	K562	blood:
8	chr19:55626847..55629043-chr19:56136358..56138081,2	MCF-7	breast:
9	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:

Variant related genes	Relation type
ZNF784	TF binding region
ENSG00000173581	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000125503	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs57728680	1.00[AMR][1000 genomes]
rs59103531	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59221728	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59316024	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59565463	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60314355	1.00[AMR][1000 genomes]
rs60831229	1.00[AMR][1000 genomes]
rs61540783	1.00[AMR][1000 genomes]
rs7256736	1.00[AMR][1000 genomes]
rs73613271	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73613277	1.00[AMR][1000 genomes]
rs73613287	0.81[AFR][1000 genomes]
rs73613290	1.00[AMR][1000 genomes]
rs73613291	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615028	1.00[AMR][1000 genomes]
rs73615038	1.00[AMR][1000 genomes]
rs73615044	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615090	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription 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	86 gene(s)	inside rSNPs	diseases
10	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56136400-56138400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:56136400-56138800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:56136400-56138800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr19:56136400-56139000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr19:56136400-56145600	Weak transcription	Right Atrium	heart
6	chr19:56136400-56146200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:56136600-56137800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr19:56136600-56138200	Enhancers	Fetal Intestine Small	intestine
9	chr19:56136600-56138800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:56136600-56138800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr19:56136600-56138800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr19:56136600-56138800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:56136600-56138800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:56136600-56138800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:56136600-56138800	Enhancers	Fetal Thymus	thymus
16	chr19:56136600-56138800	Weak transcription	Spleen	Spleen
17	chr19:56136600-56143000	Weak transcription	Stomach Mucosa	stomach
18	chr19:56136600-56143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:56136800-56137800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:56136800-56137800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:56136800-56138000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr19:56136800-56138600	Enhancers	GM12878-XiMat	blood
23	chr19:56136800-56143000	Weak transcription	HepG2	liver
24	chr19:56136800-56143200	Weak transcription	Fetal Heart	heart
25	chr19:56136800-56143200	Weak transcription	Fetal Intestine Large	intestine
26	chr19:56136800-56143200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr19:56136800-56143600	Weak transcription	Colonic Mucosa	Colon
28	chr19:56136800-56144000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:56136800-56144000	Weak transcription	NHDF-Ad	bronchial
30	chr19:56136800-56145200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:56136800-56145200	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:56136800-56145600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:56137000-56144000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:56137200-56145800	Weak transcription	Fetal Brain Female	brain
35	chr19:56137400-56137800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr19:56137600-56137800	Enhancers	Brain Germinal Matrix	brain
37	chr19:56137600-56137800	Flanking Active TSS	Thymus	Thymus
38	chr19:56137600-56138000	Active TSS	Duodenum Mucosa	Duodenum
39	chr19:56137600-56138400	Flanking Active TSS	Primary T cells from cord blood	blood

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