Variant report

Variant	rs1808661
Chromosome Location	chr19:39423953-39423954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39423891-39424665	K562	blood:	n/a	n/a
2	POLR2A	chr19:39418846-39427915	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39423918-39424625	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39423923-39424936	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:39422843-39424605	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:39419835-39427960	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:39423940-39424585	HepG2	liver:	n/a	n/a
8	CTCF	chr19:39423053-39424019	A549	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39416038..39418254-chr19:39423226..39425475,2	K562	blood:
2	chr19:39421083..39425618-chr19:39435632..39441753,7	MCF-7	breast:
3	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
4	chr19:39415679..39418451-chr19:39423572..39425396,2	MCF-7	breast:
5	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
6	chr19:39413074..39415034-chr19:39423613..39425226,2	K562	blood:
7	chr19:39326460..39328374-chr19:39422755..39424335,2	MCF-7	breast:
8	chr19:39422663..39425389-chr19:39427254..39430222,2	MCF-7	breast:
9	chr19:39332856..39334895-chr19:39423283..39424833,2	MCF-7	breast:

No data

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000104825	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000269486	Chromatin interaction
ENSG00000269190	Chromatin interaction
ENSG00000269547	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10416055	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10425217	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10775533	0.81[EUR][1000 genomes]
rs11083489	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11668245	0.85[EUR][1000 genomes]
rs12462710	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12972986	0.93[EUR][1000 genomes]
rs12982957	0.84[EUR][1000 genomes]
rs17545254	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1808662	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1865047	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1865049	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4801971	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803034	0.85[EUR][1000 genomes]
rs575	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7257007	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs730078	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7508411	0.85[EUR][1000 genomes]
rs7508539	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8113389	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9749516	0.85[EUR][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1808661	CTC-360G5.9	cis	Nerve Tibial	GTEx
rs1808661	CTC-360G5.9	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39424200	Weak transcription	Small Intestine	intestine
2	chr19:39422400-39424400	Strong transcription	Fetal Intestine Small	intestine
3	chr19:39422400-39426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:39422400-39434600	Weak transcription	Fetal Kidney	kidney
5	chr19:39422400-39435000	Weak transcription	Fetal Lung	lung
6	chr19:39422400-39435000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
8	chr19:39422600-39424400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:39422600-39425200	Weak transcription	Primary B cells from cord blood	blood
10	chr19:39422600-39425200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:39422600-39425200	Weak transcription	Stomach Mucosa	stomach
12	chr19:39422600-39427000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:39422600-39430200	Weak transcription	HUVEC	blood vessel
14	chr19:39422600-39430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:39422600-39435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:39422600-39435200	Weak transcription	HSMM	muscle
17	chr19:39422600-39440200	Weak transcription	NH-A	brain
18	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
20	chr19:39422800-39424000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:39422800-39424200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:39422800-39424400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr19:39422800-39424400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
24	chr19:39422800-39424400	ZNF genes & repeats	K562	blood
25	chr19:39422800-39424800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:39422800-39425200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:39422800-39425400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:39422800-39425600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:39422800-39432600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:39423000-39424200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:39423000-39424200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr19:39423000-39424200	Strong transcription	Ovary	ovary
33	chr19:39423000-39424400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr19:39423000-39424400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:39423000-39424400	Strong transcription	Brain Angular Gyrus	brain
36	chr19:39423000-39424400	Strong transcription	Fetal Brain Female	brain
37	chr19:39423000-39424600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:39423000-39424600	Genic enhancers	Pancreas	Pancrea
39	chr19:39423000-39424800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:39423000-39424800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:39423000-39424800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:39423000-39424800	Strong transcription	Brain Substantia Nigra	brain
43	chr19:39423000-39424800	Strong transcription	Fetal Thymus	thymus
44	chr19:39423000-39425200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr19:39423000-39425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr19:39423000-39425200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:39423000-39425400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr19:39423000-39425400	Strong transcription	Fetal Stomach	stomach
49	chr19:39423000-39425600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:39423000-39425800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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