Variant report

Variant	rs584405
Chromosome Location	chr19:56183619-56183620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr19:56183504-56184175	K562	blood:	n/a	n/a
2	CEBPB	chr19:56183324-56184434	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56181298..56183731-chr19:59054697..59056845,2	K562	blood:
2	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
3	chr19:56182120..56185364-chr19:56187275..56191666,5	MCF-7	breast:
4	chr19:56182358..56184024-chr19:56184712..56187207,2	MCF-7	breast:
5	chr19:56172205..56174377-chr19:56183143..56185111,2	MCF-7	breast:

No data

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000264910	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000267523	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10402618	0.97[ASN][1000 genomes]
rs10403866	0.89[ASN][1000 genomes]
rs10408613	0.86[ASN][1000 genomes]
rs10410404	0.82[ASN][1000 genomes]
rs10410802	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10410886	0.81[ASN][1000 genomes]
rs10412050	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10415521	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10417539	0.89[ASN][1000 genomes]
rs10421319	0.81[ASN][1000 genomes]
rs11882031	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280255	0.87[ASN][1000 genomes]
rs2287791	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28375493	0.82[ASN][1000 genomes]
rs28385383	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28595590	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28668166	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs310437	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs310441	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310472	0.82[ASN][1000 genomes]
rs3745446	0.88[ASN][1000 genomes]
rs4801526	0.88[ASN][1000 genomes]
rs523509	0.93[ASN][1000 genomes]
rs57544196	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58490076	0.86[ASN][1000 genomes]
rs60873246	0.87[ASN][1000 genomes]
rs617073	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648651	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs681804	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256441	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73613281	0.89[ASN][1000 genomes]
rs8100143	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8104242	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109983	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv828644	chr19:56183529-56184218	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56170000-56184800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56170200-56184000	Strong transcription	Primary T cells from cord blood	blood
3	chr19:56170200-56185200	Strong transcription	Fetal Thymus	thymus
4	chr19:56170200-56185400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr19:56170200-56185800	Strong transcription	Fetal Stomach	stomach
6	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
8	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
10	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
11	chr19:56171200-56184600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:56171400-56185000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:56171400-56185400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:56172000-56185000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:56172200-56185000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:56172600-56186000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:56172800-56184800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:56175400-56185600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr19:56175800-56186000	Weak transcription	Fetal Kidney	kidney
20	chr19:56178000-56185800	Weak transcription	HSMMtube	muscle
21	chr19:56178600-56185800	Weak transcription	Fetal Brain Male	brain
22	chr19:56179800-56184800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:56179800-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:56179800-56185400	Strong transcription	NHEK	skin
25	chr19:56180200-56185600	Genic enhancers	Dnd41	blood
26	chr19:56181200-56184200	Strong transcription	Hela-S3	cervix
27	chr19:56181600-56184000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:56181600-56184000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:56181600-56185800	Genic enhancers	Liver	Liver
30	chr19:56181800-56185400	Strong transcription	GM12878-XiMat	blood
31	chr19:56182000-56183800	Weak transcription	HUVEC	blood vessel
32	chr19:56182000-56184000	Strong transcription	Colonic Mucosa	Colon
33	chr19:56182000-56184200	Strong transcription	Lung	lung
34	chr19:56182000-56184400	Strong transcription	HepG2	liver
35	chr19:56182000-56184800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr19:56182000-56184800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:56182000-56184800	Weak transcription	Fetal Lung	lung
38	chr19:56182000-56185200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr19:56182000-56185200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:56182000-56185200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:56182000-56185200	Strong transcription	Fetal Muscle Leg	muscle
42	chr19:56182000-56185400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:56182000-56185600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:56182000-56185600	Weak transcription	HSMM	muscle
45	chr19:56182000-56185800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:56182000-56185800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:56182000-56185800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:56182000-56185800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:56182000-56185800	Strong transcription	Fetal Intestine Large	intestine
50	chr19:56182000-56185800	Strong transcription	Fetal Intestine Small	intestine

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