Variant report

Variant	rs506782
Chromosome Location	chr19:56595551-56595552
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56594686..56596745-chr19:56823660..56825677,2	K562	blood:
2	chr19:56594696..56597822-chr19:56630951..56634176,4	K562	blood:

Variant related genes	Relation type
ENSG00000142409	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267298	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12459102	0.94[EUR][1000 genomes]
rs2631637	0.82[EUR][1000 genomes]
rs2631640	0.94[EUR][1000 genomes]
rs478402	0.82[EUR][1000 genomes]
rs481936	0.88[EUR][1000 genomes]
rs492078	0.94[EUR][1000 genomes]
rs501798	0.88[EUR][1000 genomes]
rs504350	0.94[EUR][1000 genomes]
rs517582	0.94[EUR][1000 genomes]
rs521092	0.94[EUR][1000 genomes]
rs524778	0.94[EUR][1000 genomes]
rs524829	0.94[EUR][1000 genomes]
rs526275	0.82[EUR][1000 genomes]
rs530102	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs533640	0.94[EUR][1000 genomes]
rs533734	0.94[EUR][1000 genomes]
rs535393	0.94[EUR][1000 genomes]
rs536342	0.94[EUR][1000 genomes]
rs536414	0.88[EUR][1000 genomes]
rs537425	0.94[EUR][1000 genomes]
rs540900	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs554681	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564050	0.94[EUR][1000 genomes]
rs578990	0.94[EUR][1000 genomes]
rs582271	0.94[EUR][1000 genomes]
rs588574	0.94[EUR][1000 genomes]
rs592827	0.82[EUR][1000 genomes]
rs604364	0.90[AMR][1000 genomes]
rs609736	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs609755	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs619934	0.94[EUR][1000 genomes]
rs630704	0.94[EUR][1000 genomes]
rs642776	0.83[AMR][1000 genomes]
rs648352	0.94[EUR][1000 genomes]
rs665846	0.94[EUR][1000 genomes]
rs667438	0.94[EUR][1000 genomes]
rs668056	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677142	0.94[EUR][1000 genomes]
rs684653	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1062406	chr19:56382492-56602374	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1058988	chr19:56382492-56609032	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
7	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS 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	47 gene(s)	inside rSNPs	diseases
11	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56578200-56596800	Weak transcription	Gastric	stomach
2	chr19:56592600-56596200	Weak transcription	A549	lung
3	chr19:56592600-56596800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56592600-56599400	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:56592600-56599800	Weak transcription	Aorta	Aorta
6	chr19:56592600-56600000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:56592600-56600000	Weak transcription	Hela-S3	cervix
8	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
9	chr19:56592800-56596200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:56592800-56596200	Weak transcription	Thymus	Thymus
11	chr19:56592800-56596600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:56592800-56596600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:56592800-56596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:56592800-56596600	Weak transcription	Esophagus	oesophagus
15	chr19:56592800-56596600	Weak transcription	Lung	lung
16	chr19:56592800-56596800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:56592800-56597400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:56592800-56597600	Weak transcription	Brain Germinal Matrix	brain
19	chr19:56592800-56598000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:56592800-56598600	Weak transcription	Ovary	ovary
21	chr19:56592800-56599800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:56592800-56600000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:56592800-56600000	Weak transcription	Dnd41	blood
24	chr19:56592800-56601200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr19:56592800-56602200	Weak transcription	NH-A	brain
26	chr19:56592800-56602400	Weak transcription	Brain Anterior Caudate	brain
27	chr19:56592800-56602800	Weak transcription	Right Atrium	heart
28	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:56593000-56595600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:56593000-56596200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:56593000-56596200	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:56593000-56596200	Weak transcription	HMEC	breast
33	chr19:56593000-56596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:56593000-56596600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:56593000-56596600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:56593000-56596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr19:56593000-56596600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:56593000-56596600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:56593000-56596600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:56593000-56596600	Weak transcription	Left Ventricle	heart
41	chr19:56593000-56596800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:56593000-56596800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:56593000-56596800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr19:56593000-56596800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:56593000-56597000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:56593000-56598600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr19:56593000-56599800	Weak transcription	Adipose Nuclei	Adipose
48	chr19:56593000-56599800	Weak transcription	Liver	Liver
49	chr19:56593000-56599800	Weak transcription	Brain Angular Gyrus	brain
50	chr19:56593000-56599800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links