Variant report

Variant	rs58842178
Chromosome Location	chr19:18634764-18634765
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:10)
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	POLR2A	chr19:18634584-18634856	HepG2	liver:	n/a	n/a
2	CEBPB	chr19:18634581-18634956	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18629832..18635572-chr19:18680910..18686315,11	K562	blood:
2	chr19:18630875..18635401-chr19:18651200..18655863,9	MCF-7	breast:
3	chr19:18634527..18636637-chr19:18667568..18669248,2	K562	blood:
4	chr19:18630919..18637145-chr19:18698949..18704438,10	K562	blood:
5	chr19:18633212..18634980-chr19:18648549..18650137,2	K562	blood:
6	chr19:18629959..18634840-chr19:18652830..18656407,13	K562	blood:
7	chr19:18633341..18635579-chr19:18650519..18652255,2	K562	blood:
8	chr19:18630485..18634839-chr19:18666846..18671916,7	MCF-7	breast:
9	chr19:18632022..18634941-chr19:18640789..18642587,3	K562	blood:
10	chr19:18631257..18635225-chr19:18680941..18684038,5	MCF-7	breast:

No data

Variant related genes	Relation type
ELL	TF binding region
ENSG00000006015	Chromatin interaction
ENSG00000268938	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000105700	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11574806	0.87[EUR][1000 genomes]
rs16982418	1.00[EUR][1000 genomes]
rs16982427	1.00[EUR][1000 genomes]
rs16982429	1.00[EUR][1000 genomes]
rs16982485	1.00[EUR][1000 genomes]
rs2314669	0.87[EUR][1000 genomes]
rs34078075	1.00[EUR][1000 genomes]
rs34868531	1.00[EUR][1000 genomes]
rs35328461	1.00[EUR][1000 genomes]
rs58410315	1.00[EUR][1000 genomes]
rs58604797	1.00[EUR][1000 genomes]
rs58723610	1.00[EUR][1000 genomes]
rs59511380	1.00[EUR][1000 genomes]
rs59549953	1.00[EUR][1000 genomes]
rs60687616	1.00[EUR][1000 genomes]
rs61743938	1.00[EUR][1000 genomes]
rs61743954	0.87[EUR][1000 genomes]
rs7247603	0.87[EUR][1000 genomes]
rs73523072	0.87[EUR][1000 genomes]
rs73523074	0.87[EUR][1000 genomes]
rs8101976	1.00[EUR][1000 genomes]
rs8102397	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
5	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 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	chr19:18632800-18641000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:18632800-18642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:18632800-18642200	Weak transcription	Aorta	Aorta
4	chr19:18632800-18652200	Weak transcription	Fetal Heart	heart
5	chr19:18632800-18652800	Weak transcription	Stomach Mucosa	stomach
6	chr19:18632800-18654600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:18633000-18637000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:18633000-18637200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:18633000-18638600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:18633000-18640400	Weak transcription	Right Ventricle	heart
11	chr19:18633000-18640400	Weak transcription	Spleen	Spleen
12	chr19:18633000-18642000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18633000-18642000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:18633000-18642000	Weak transcription	Lung	lung
15	chr19:18633000-18642200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:18633000-18642200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:18633000-18642200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:18633000-18642200	Weak transcription	Liver	Liver
19	chr19:18633000-18642200	Weak transcription	Colonic Mucosa	Colon
20	chr19:18633000-18642200	Weak transcription	Esophagus	oesophagus
21	chr19:18633000-18642200	Weak transcription	Gastric	stomach
22	chr19:18633000-18642200	Weak transcription	Left Ventricle	heart
23	chr19:18633000-18642200	Weak transcription	Pancreas	Pancrea
24	chr19:18633000-18642200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:18633000-18642200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:18633000-18642800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:18633000-18653400	Weak transcription	Psoas Muscle	Psoas
28	chr19:18633200-18637200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:18633200-18640400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:18633200-18653200	Weak transcription	Right Atrium	heart
31	chr19:18633600-18635000	Flanking Active TSS	HepG2	liver
32	chr19:18633600-18640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:18633600-18640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:18633600-18642200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:18633600-18642200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:18633600-18642200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:18633600-18642200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:18633600-18642200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:18633600-18642200	Weak transcription	HSMMtube	muscle
40	chr19:18633600-18642200	Weak transcription	NHLF	lung
41	chr19:18633600-18645200	Weak transcription	HSMM	muscle
42	chr19:18633600-18646600	Weak transcription	Small Intestine	intestine
43	chr19:18633800-18634800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:18633800-18636800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:18633800-18636800	Weak transcription	HMEC	breast
46	chr19:18633800-18636800	Weak transcription	NHEK	skin
47	chr19:18633800-18637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:18633800-18640200	Weak transcription	Fetal Stomach	stomach
49	chr19:18633800-18640400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:18633800-18640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links