Variant report

Variant	rs2280254
Chromosome Location	chr19:56125944-56125945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56091961..56094191-chr19:56125240..56128185,2	K562	blood:
2	chr19:56038107..56040366-chr19:56125681..56127258,2	K562	blood:
3	chr17:57182542..57185002-chr19:56124055..56126048,2	MCF-7	breast:
4	chr19:56123945..56128950-chr19:56130054..56135521,12	K562	blood:
5	chr19:56112593..56114328-chr19:56123859..56126388,2	K562	blood:
6	chr19:56125784..56127502-chr19:56144070..56146807,2	K562	blood:
7	chr19:56125664..56128037-chr19:56135506..56137202,2	MCF-7	breast:
8	chr19:56115478..56119505-chr19:56121747..56126815,6	K562	blood:
9	chr19:56110092..56111960-chr19:56124082..56126153,2	K562	blood:
10	chr19:56119981..56122745-chr19:56123136..56127076,6	K562	blood:
11	chr19:56125033..56127900-chr19:56132851..56135429,4	MCF-7	breast:
12	chr19:56122149..56126669-chr19:56127522..56130662,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171443	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000224738	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12460543	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292810	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292811	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34318926	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34907477	0.87[ASN][1000 genomes]
rs35763366	0.89[EUR][1000 genomes]
rs3852898	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57314044	0.86[ASN][1000 genomes]
rs751729	0.89[ASN][1000 genomes]
rs8110652	0.87[ASN][1000 genomes]
rs908668	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56118200-56135000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:56118400-56126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:56118400-56126000	Weak transcription	Brain Substantia Nigra	brain
4	chr19:56118400-56126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:56118400-56127000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:56118400-56127400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:56118400-56128800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:56118400-56134400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:56118400-56135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:56118400-56135200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:56118400-56135200	Weak transcription	HUVEC	blood vessel
12	chr19:56118600-56126000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:56118600-56127400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:56118600-56128800	Weak transcription	Stomach Mucosa	stomach
15	chr19:56118600-56129600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:56118600-56129800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:56118600-56131600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:56118600-56131800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:56118600-56134800	Strong transcription	Fetal Intestine Small	intestine
20	chr19:56118600-56134800	Weak transcription	K562	blood
21	chr19:56118600-56135200	Weak transcription	Fetal Brain Male	brain
22	chr19:56118800-56127600	Weak transcription	HMEC	breast
23	chr19:56118800-56129400	Strong transcription	Thymus	Thymus
24	chr19:56118800-56131000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:56119600-56134000	Weak transcription	HepG2	liver
26	chr19:56119600-56134800	Weak transcription	Hela-S3	cervix
27	chr19:56120200-56129400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:56120400-56129400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:56120800-56129200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:56120800-56129400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:56121000-56129200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:56121200-56135000	Weak transcription	NH-A	brain
33	chr19:56121400-56127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:56121400-56129400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:56121400-56129800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:56121600-56126000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:56121600-56126000	Weak transcription	Liver	Liver
38	chr19:56121600-56126000	Weak transcription	Osteobl	bone
39	chr19:56121600-56126600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr19:56121600-56127000	Weak transcription	HSMMtube	muscle
41	chr19:56121600-56129600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:56121600-56130600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:56121600-56131600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:56121600-56134000	Strong transcription	Fetal Brain Female	brain
45	chr19:56121600-56135800	Weak transcription	NHDF-Ad	bronchial
46	chr19:56121800-56128800	Weak transcription	Fetal Kidney	kidney
47	chr19:56121800-56130400	Strong transcription	Fetal Stomach	stomach
48	chr19:56122200-56126000	Weak transcription	NHEK	skin
49	chr19:56122200-56126400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:56122200-56126600	Weak transcription	Rectal Mucosa Donor 29	rectum

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