Variant report

Variant	rs28444246
Chromosome Location	chr19:38665378-38665379
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38660108..38661702-chr19:38665066..38666638,2	MCF-7	breast:
2	chr19:38659478..38661172-chr19:38664692..38666456,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10401165	0.94[EUR][1000 genomes]
rs10420506	0.93[EUR][1000 genomes]
rs28495744	0.93[EUR][1000 genomes]
rs4803828	0.95[EUR][1000 genomes]
rs4803829	0.93[EUR][1000 genomes]
rs6508767	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7245788	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7256332	0.93[EUR][1000 genomes]
rs73627654	0.93[EUR][1000 genomes]
rs73627663	0.89[EUR][1000 genomes]
rs73627676	0.92[EUR][1000 genomes]
rs73627686	0.85[EUR][1000 genomes]
rs73930553	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28444246	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38653600-38668600	Strong transcription	Primary B cells from peripheral blood	blood
3	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
4	chr19:38653800-38666600	Strong transcription	A549	lung
5	chr19:38653800-38670800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:38655200-38669400	Weak transcription	Fetal Lung	lung
7	chr19:38656200-38675200	Weak transcription	Stomach Mucosa	stomach
8	chr19:38656400-38670400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:38656400-38670400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:38656400-38670800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:38656400-38671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:38656400-38674000	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:38656800-38669400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:38657400-38665800	Weak transcription	NHLF	lung
15	chr19:38657600-38673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:38657600-38673800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:38657800-38669600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:38658400-38674000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:38658400-38684800	Weak transcription	HepG2	liver
21	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:38658600-38670800	Weak transcription	Fetal Brain Female	brain
23	chr19:38658800-38669200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr19:38658800-38669400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr19:38658800-38669400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:38658800-38670400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr19:38659600-38666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38659600-38666400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:38659600-38668800	Weak transcription	Primary B cells from cord blood	blood
30	chr19:38659600-38673600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:38659600-38673600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:38659800-38669400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:38659800-38670600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:38660400-38669600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:38661000-38669400	Weak transcription	Liver	Liver
36	chr19:38661000-38673200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:38661200-38668800	Weak transcription	Thymus	Thymus
38	chr19:38661200-38669400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:38661200-38670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:38661200-38671200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:38661200-38673600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:38661400-38665800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:38661400-38669400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr19:38661400-38682600	Weak transcription	Aorta	Aorta
45	chr19:38661600-38670400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:38661600-38671600	Weak transcription	Osteobl	bone
47	chr19:38661600-38673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:38661600-38674000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:38661800-38682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:38662200-38666400	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links