Variant report

Variant	rs73048670
Chromosome Location	chr19:44284531-44284532
allele	C/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	CTCF	chr19:44283519-44285246	A549	lung:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
2	ZNF263	chr19:44284130-44285070	K562	blood:	n/a	chr19:44284533-44284554 chr19:44284496-44284517
3	FOXA2	chr19:44283919-44284568	A549	lung:	n/a	n/a
4	EBF1	chr19:44284040-44284592	GM12878	blood:	n/a	chr19:44284327-44284338
5	ZBTB7A	chr19:44284021-44284547	K562	blood:	n/a	n/a
6	POLR2A	chr19:44283508-44284586	HCT-116	colon:	n/a	n/a
7	POLR2A	chr19:44282566-44285595	GM12878	blood:	n/a	n/a
8	CTCF	chr19:44283925-44284537	K562	blood:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
9	MTA3	chr19:44282570-44284543	GM12878	blood:	n/a	n/a
10	ZBTB7A	chr19:44283850-44285459	K562	blood:	n/a	n/a
11	ZNF263	chr19:44284212-44284696	HEK293-T-REx	kidney:	n/a	chr19:44284533-44284554 chr19:44284496-44284517
12	POLR2A	chr19:44284428-44284564	K562	blood:	n/a	n/a
13	MAZ	chr19:44282811-44284539	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:44284472-44284550	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44258057..44261358-chr19:44282388..44285287,3	MCF-7	breast:
2	chr19:44269561..44270470-chr19:44283736..44284661,2	MCF-7	breast:
3	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
4	chr19:44270615..44271921-chr19:44283761..44284756,6	MCF-7	breast:
5	chr19:44256245..44259869-chr19:44284477..44291035,7	MCF-7	breast:

Variant related genes	Relation type
KCNN4	TF binding region
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10401170	0.81[ASN][1000 genomes]
rs10401203	0.81[ASN][1000 genomes]
rs10426528	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11083720	0.89[ASN][1000 genomes]
rs11879798	0.95[ASN][1000 genomes]
rs349046	0.81[ASN][1000 genomes]
rs349047	0.81[ASN][1000 genomes]
rs349048	0.81[ASN][1000 genomes]
rs349049	0.81[ASN][1000 genomes]
rs349050	0.81[ASN][1000 genomes]
rs349053	0.81[ASN][1000 genomes]
rs56344893	0.97[ASN][1000 genomes]
rs56681946	0.97[ASN][1000 genomes]
rs62116961	0.93[ASN][1000 genomes]
rs62116990	0.81[ASN][1000 genomes]
rs8104447	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8111664	0.80[EUR][1000 genomes];0.81[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73048670	KCNN4	cis	Whole Blood	GTEx
rs73048670	LYPD5	cis	Skin Sun Exposed Lower leg	GTEx
rs73048670	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44280800-44284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44280800-44285800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:44281000-44284600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr19:44281200-44285600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:44281400-44287000	Enhancers	Spleen	Spleen
6	chr19:44281800-44285400	Active TSS	Rectal Smooth Muscle	rectum
7	chr19:44281800-44285600	Enhancers	Fetal Intestine Large	intestine
8	chr19:44282000-44285600	Enhancers	Lung	lung
9	chr19:44282200-44284800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:44282200-44286800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44282400-44284800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr19:44282400-44285000	Weak transcription	NHDF-Ad	bronchial
13	chr19:44282400-44289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:44282600-44284600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:44282800-44284600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:44282800-44284600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:44282800-44285800	Flanking Active TSS	Placenta	Placenta
18	chr19:44283000-44284600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr19:44283000-44284600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:44283000-44284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:44283000-44285000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:44283000-44285200	Flanking Active TSS	Colonic Mucosa	Colon
23	chr19:44283000-44285400	Flanking Active TSS	Fetal Thymus	thymus
24	chr19:44283000-44286000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:44283200-44284600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr19:44283200-44284600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr19:44283200-44285000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr19:44283200-44285600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:44283400-44284800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:44283400-44284800	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:44283400-44284800	Enhancers	Fetal Intestine Small	intestine
32	chr19:44283400-44284800	Weak transcription	Fetal Muscle Leg	muscle
33	chr19:44283400-44285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:44283400-44285200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:44283400-44285200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr19:44283600-44284600	Enhancers	Fetal Muscle Trunk	muscle
37	chr19:44283600-44284800	Active TSS	Primary T cells from cord blood	blood
38	chr19:44283600-44284800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:44283600-44284800	Enhancers	HSMM	muscle
40	chr19:44283600-44285000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:44283800-44284800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:44283800-44284800	Enhancers	HepG2	liver
43	chr19:44283800-44285000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:44283800-44285200	Active TSS	Small Intestine	intestine
45	chr19:44283800-44285400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:44283800-44285400	Active TSS	HMEC	breast
47	chr19:44283800-44285800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr19:44284000-44284600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:44284000-44284800	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr19:44284000-44284800	Weak transcription	Esophagus	oesophagus

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