Variant report

Variant	rs28620146
Chromosome Location	chr19:39985015-39985016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39984952-39985092	K562	blood:	n/a	n/a
3	SIN3AK20	chr19:39981974-39985585	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39984438-39985220	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:39984544-39985602	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:39973155-39985792	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:39925083..39926660-chr19:39982191..39985073,2	K562	blood:
2	chr19:39950586..39952165-chr19:39983591..39985551,2	K562	blood:
3	chr19:39982701..39986911-chr19:39987055..39990908,4	MCF-7	breast:
4	chr19:39975925..39978735-chr19:39983543..39985534,2	MCF-7	breast:

No data

Variant related genes	Relation type
DLL3	TF binding region
ENSG00000105197	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000105193	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10423537	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2060272	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2288933	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2288934	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304219	0.81[AMR][1000 genomes]
rs2304221	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34918990	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35647910	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803245	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803246	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803247	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508864	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508865	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251384	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8111260	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28620146	RPS16	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
3	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
4	chr19:39980000-39988600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:39980600-39988600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:39980800-39986600	Weak transcription	NHLF	lung
7	chr19:39980800-39988200	Weak transcription	HUVEC	blood vessel
8	chr19:39980800-39988400	Weak transcription	K562	blood
9	chr19:39981000-39985200	Weak transcription	Brain Substantia Nigra	brain
10	chr19:39981000-39985400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:39981000-39985600	Weak transcription	Esophagus	oesophagus
12	chr19:39981000-39986200	Weak transcription	HepG2	liver
13	chr19:39981000-39986600	Weak transcription	NH-A	brain
14	chr19:39981000-39988200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:39981000-39988400	Weak transcription	Aorta	Aorta
16	chr19:39981000-39988400	Weak transcription	GM12878-XiMat	blood
17	chr19:39981000-39988400	Weak transcription	HSMMtube	muscle
18	chr19:39981000-39988600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:39981000-39988600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:39981000-39988600	Weak transcription	Gastric	stomach
21	chr19:39981000-39988800	Weak transcription	Pancreas	Pancrea
22	chr19:39981200-39985200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:39981200-39985200	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:39981200-39985600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:39981200-39985800	Weak transcription	Lung	lung
26	chr19:39981200-39986000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:39981200-39988400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr19:39981400-39985200	Weak transcription	Brain Angular Gyrus	brain
29	chr19:39981400-39985200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:39981400-39985400	Weak transcription	Fetal Lung	lung
31	chr19:39981400-39985600	Weak transcription	Fetal Intestine Large	intestine
32	chr19:39981400-39986000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr19:39981400-39986000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr19:39981400-39986200	Weak transcription	Dnd41	blood
35	chr19:39981400-39986600	Weak transcription	Fetal Thymus	thymus
36	chr19:39981400-39988200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:39981400-39988400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:39981400-39988600	Weak transcription	Primary B cells from cord blood	blood
39	chr19:39981400-39988600	Weak transcription	HSMM	muscle
40	chr19:39981600-39986800	Weak transcription	Osteobl	bone
41	chr19:39981600-39988400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:39981800-39985200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:39981800-39985800	Weak transcription	Placenta	Placenta
44	chr19:39982000-39985200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr19:39982800-39986000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:39982800-39986600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:39982800-39986800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:39982800-39986800	Weak transcription	Adipose Nuclei	Adipose
49	chr19:39982800-39987600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:39983000-39985200	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links