Variant report

Variant	rs56296628
Chromosome Location	chr19:43995398-43995399
allele	G/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	POLR2A	chr19:43994294-43995545	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:43995298..43997573-chr19:44007651..44009596,2	MCF-7	breast:

Variant related genes	Relation type
PHLDB3	TF binding region
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11083710	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11879973	1.00[EUR][1000 genomes]
rs55908340	1.00[EUR][1000 genomes]
rs56284822	1.00[EUR][1000 genomes]
rs59051447	1.00[EUR][1000 genomes]
rs61732260	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73935005	1.00[EUR][1000 genomes]
rs73935006	1.00[EUR][1000 genomes]
rs73937413	1.00[EUR][1000 genomes]
rs73937427	1.00[EUR][1000 genomes]
rs73937428	1.00[EUR][1000 genomes]
rs9653099	1.00[EUR][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	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv3417194	chr19:43975161-44000760	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv2762041	chr19:43986023-44014457	Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43970000-43998200	Weak transcription	Gastric	stomach
2	chr19:43973800-43999800	Weak transcription	HepG2	liver
3	chr19:43979600-44005800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:43979800-43998400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:43979800-43998600	Weak transcription	Lung	lung
6	chr19:43979800-43998800	Weak transcription	Aorta	Aorta
7	chr19:43979800-43998800	Weak transcription	Pancreas	Pancrea
8	chr19:43980000-43998600	Weak transcription	Brain Germinal Matrix	brain
9	chr19:43980000-43998600	Weak transcription	Fetal Brain Female	brain
10	chr19:43980000-43998800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:43980000-43999400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:43980000-43999400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:43980000-43999600	Weak transcription	Brain Angular Gyrus	brain
14	chr19:43980000-43999600	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:43980000-44001000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:43980000-44001000	Weak transcription	Fetal Lung	lung
17	chr19:43980000-44001200	Weak transcription	Brain Substantia Nigra	brain
18	chr19:43980000-44001200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:43980000-44005600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:43980000-44005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:43980000-44006200	Weak transcription	HMEC	breast
22	chr19:43980200-43999600	Weak transcription	Adipose Nuclei	Adipose
23	chr19:43980200-44001000	Weak transcription	Fetal Thymus	thymus
24	chr19:43980400-43998200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:43980400-43998800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:43980400-43999000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:43980400-43999200	Weak transcription	Placenta	Placenta
28	chr19:43980400-43999800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:43980400-44000400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr19:43980400-44001200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:43980800-43998200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:43980800-44007400	Weak transcription	HSMM	muscle
33	chr19:43981000-43998800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:43981200-43998800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:43981200-44007200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:43981400-43999200	Weak transcription	NHDF-Ad	bronchial
37	chr19:43981400-44000400	Weak transcription	Osteobl	bone
38	chr19:43981400-44007200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:43982600-43998400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:43982600-43998800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:43982600-43998800	Weak transcription	NHLF	lung
42	chr19:43982600-43999000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:43982600-43999600	Weak transcription	Brain Hippocampus Middle	brain
44	chr19:43982800-43998600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:43982800-44006800	Weak transcription	K562	blood
46	chr19:43983600-44005800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:43984200-43998800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:43985200-43997600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:43985400-43998600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:43986600-43998200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links