Variant report

Variant	rs59343080
Chromosome Location	chr19:40734673-40734674
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr19:40731136-40743299	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:40734654-40735236	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:40734245-40734795	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:40733354-40739269	K562	blood:	n/a	n/a
5	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:40733628-40734695	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:40733947-40734741	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40729308..40731117-chr19:40732783..40735609,2	K562	blood:
2	chr19:40730620..40735723-chr19:40738673..40743679,8	MCF-7	breast:
3	chr19:40734116..40737610-chr19:40738895..40742001,3	MCF-7	breast:
4	chr15:77925887..77926426-chr19:40734602..40735348,2	MCF-7	breast:
5	chr19:40732606..40735043-chr19:40736232..40738956,2	K562	blood:

No data

Variant related genes	Relation type
CNTD2	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000105219	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10408356	0.82[ASN][1000 genomes]
rs10415181	0.81[ASN][1000 genomes]
rs10416620	0.84[ASN][1000 genomes]
rs10418932	0.84[ASN][1000 genomes]
rs10419465	0.84[ASN][1000 genomes]
rs16974157	0.89[ASN][1000 genomes]
rs2163840	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2304185	0.80[ASN][1000 genomes]
rs2304188	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28362958	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34716810	0.84[ASN][1000 genomes]
rs55862427	0.82[ASN][1000 genomes]
rs58336440	0.89[ASN][1000 genomes]
rs59010363	0.89[ASN][1000 genomes]
rs61685259	0.82[ASN][1000 genomes]
rs62107590	0.89[ASN][1000 genomes]
rs62107593	0.84[ASN][1000 genomes]
rs62107594	0.84[ASN][1000 genomes]
rs7254617	0.84[ASN][1000 genomes]
rs8111619	0.84[ASN][1000 genomes]
rs892118	0.89[ASN][1000 genomes]
rs892119	0.82[ASN][1000 genomes]
rs892120	0.82[ASN][1000 genomes]
rs9304588	0.84[ASN][1000 genomes]
rs9304589	0.84[ASN][1000 genomes]
rs934426	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40726400-40735200	Weak transcription	K562	blood
2	chr19:40732200-40737000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:40732400-40740800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:40732600-40735000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:40732600-40735000	Weak transcription	NHDF-Ad	bronchial
6	chr19:40732600-40737000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:40732600-40737400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:40732600-40737600	Weak transcription	Brain Anterior Caudate	brain
9	chr19:40732600-40739000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:40732600-40740400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:40732800-40735000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:40732800-40735200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:40732800-40737000	Weak transcription	Spleen	Spleen
14	chr19:40732800-40737200	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:40732800-40737400	Weak transcription	Left Ventricle	heart
16	chr19:40732800-40737400	Weak transcription	Right Atrium	heart
17	chr19:40732800-40737600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr19:40732800-40737600	Weak transcription	Lung	lung
19	chr19:40732800-40737600	Weak transcription	Right Ventricle	heart
20	chr19:40732800-40738000	Weak transcription	Ovary	ovary
21	chr19:40732800-40738000	Weak transcription	Pancreas	Pancrea
22	chr19:40732800-40738000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:40732800-40738400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:40732800-40738600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:40732800-40738800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:40732800-40739200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:40732800-40740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:40732800-40740800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr19:40732800-40740800	Weak transcription	HMEC	breast
30	chr19:40732800-40759000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:40733000-40734800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr19:40733000-40735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:40733000-40735000	Weak transcription	A549	lung
34	chr19:40733000-40735600	Weak transcription	Adipose Nuclei	Adipose
35	chr19:40733000-40736000	Enhancers	HepG2	liver
36	chr19:40733000-40737000	Weak transcription	Hela-S3	cervix
37	chr19:40733000-40737400	Weak transcription	NHLF	lung
38	chr19:40733000-40737600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:40733000-40738000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:40733000-40738000	Weak transcription	Dnd41	blood
41	chr19:40733000-40739000	Enhancers	Placenta	Placenta
42	chr19:40733000-40739000	Weak transcription	Gastric	stomach
43	chr19:40733000-40740800	Weak transcription	GM12878-XiMat	blood
44	chr19:40733600-40734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:40733600-40738000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr19:40733800-40737400	Weak transcription	Fetal Stomach	stomach
47	chr19:40734000-40735200	Bivalent Enhancer	HUVEC	blood vessel
48	chr19:40734000-40737600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:40734000-40742000	Weak transcription	Small Intestine	intestine
50	chr19:40734200-40737200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links