Variant report

Variant	rs1982242
Chromosome Location	chr15:78452872-78452873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr15:78452854-78452948	PANC-1	pancreas:	n/a	n/a
2	REST	chr15:78452869-78452945	HepG2	liver:	n/a	n/a
3	REST	chr15:78452841-78452983	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78440859..78443747-chr15:78450376..78455479,5	K562	blood:
2	chr15:78445352..78447545-chr15:78452643..78454285,2	K562	blood:
3	chr15:78448588..78451426-chr15:78451804..78454242,3	MCF-7	breast:
4	chr15:78439170..78443635-chr15:78452310..78455814,4	K562	blood:

No data

Variant related genes	Relation type
IDH3A	TF binding region
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11855354	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903696	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12915990	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304824	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495275	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495276	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7172176	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8032618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034946	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920103	0.89[EUR][1000 genomes]
rs9972613	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1982242	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78442600-78458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:78442800-78463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:78443400-78453400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:78443400-78454000	Weak transcription	Fetal Kidney	kidney
6	chr15:78443400-78458000	Weak transcription	Stomach Mucosa	stomach
7	chr15:78443600-78453600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:78443600-78453600	Weak transcription	HepG2	liver
9	chr15:78443600-78453600	Weak transcription	K562	blood
10	chr15:78443600-78453600	Weak transcription	NHLF	lung
11	chr15:78444200-78453600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:78445800-78453600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:78445800-78464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:78446600-78465200	Strong transcription	Fetal Intestine Large	intestine
15	chr15:78446800-78466000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:78447200-78459600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:78447400-78459200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr15:78447600-78459600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:78447600-78464400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr15:78447800-78459000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:78447800-78459600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr15:78448000-78453800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:78448000-78459800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:78448000-78463000	Strong transcription	Fetal Muscle Leg	muscle
26	chr15:78448000-78464200	Strong transcription	Liver	Liver
27	chr15:78448000-78465200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:78448000-78465800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:78448200-78453600	Weak transcription	HSMM	muscle
30	chr15:78448400-78461000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:78448400-78461000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:78448600-78465400	Strong transcription	Placenta	Placenta
33	chr15:78448800-78454000	Weak transcription	Psoas Muscle	Psoas
34	chr15:78448800-78463000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:78448800-78464200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:78448800-78466600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:78449000-78467800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:78449200-78458400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:78449200-78458800	Strong transcription	GM12878-XiMat	blood
40	chr15:78449400-78465200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:78449600-78453600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:78449600-78453600	Weak transcription	HMEC	breast
43	chr15:78449600-78453800	Weak transcription	NHEK	skin
44	chr15:78449800-78454000	Strong transcription	Brain Anterior Caudate	brain
45	chr15:78449800-78454800	Strong transcription	Hela-S3	cervix
46	chr15:78449800-78465400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:78450000-78453400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:78450000-78453800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:78450000-78458200	Strong transcription	Thymus	Thymus
50	chr15:78450000-78458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links