Variant report

Variant	rs28422038
Chromosome Location	chr19:39468000-39468001
allele	A/G
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	chr19:39464868-39468454	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39466848..39468476-chr19:39486869..39489506,3	K562	blood:
2	chr19:39466590..39468490-chr19:39469783..39471749,2	MCF-7	breast:
3	chr19:39341802..39343679-chr19:39464849..39468129,3	K562	blood:
4	chr19:39464164..39468178-chr19:39520932..39524285,4	MCF-7	breast:

Variant related genes	Relation type
FBXO17	TF binding region
ENSG00000161243	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000267992	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10425811	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6508831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250688	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7252417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39467000-39468800	Weak transcription	HSMMtube	muscle
2	chr19:39467200-39469400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39467400-39468000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:39467400-39468400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:39467400-39468400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:39467400-39468600	Weak transcription	Placenta	Placenta
7	chr19:39467400-39468600	Weak transcription	HUVEC	blood vessel
8	chr19:39467400-39468600	Weak transcription	Osteobl	bone
9	chr19:39467400-39468800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:39467400-39468800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:39467400-39468800	Weak transcription	Pancreas	Pancrea
12	chr19:39467400-39468800	Weak transcription	NH-A	brain
13	chr19:39467400-39469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:39467400-39469400	Enhancers	Fetal Intestine Small	intestine
15	chr19:39467400-39469400	Enhancers	GM12878-XiMat	blood
16	chr19:39467400-39470000	Enhancers	Fetal Intestine Large	intestine
17	chr19:39467400-39470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:39467400-39471200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:39467600-39468200	Enhancers	Fetal Kidney	kidney
20	chr19:39467600-39468400	Enhancers	HepG2	liver
21	chr19:39467600-39468600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:39467600-39468600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:39467600-39468800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:39467600-39468800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:39467600-39469200	Enhancers	A549	lung
26	chr19:39467600-39469400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:39467600-39469400	Enhancers	Liver	Liver
28	chr19:39467600-39470400	Weak transcription	K562	blood
29	chr19:39467600-39471400	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:39467600-39471400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr19:39467800-39468200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:39467800-39468200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:39467800-39468400	Weak transcription	Fetal Stomach	stomach
34	chr19:39468000-39469200	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links