Variant report

Variant	rs6508825
Chromosome Location	chr19:39424753-39424754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39418846-39427915	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39423923-39424936	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:39419835-39427960	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39424637-39424903	K562	blood:	n/a	n/a
5	POLR2A	chr19:39424160-39424842	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39423986..39425546-chr19:39435079..39437726,2	K562	blood:
2	chr19:39416038..39418254-chr19:39423226..39425475,2	K562	blood:
3	chr19:39421083..39425618-chr19:39435632..39441753,7	MCF-7	breast:
4	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
5	chr19:39415679..39418451-chr19:39423572..39425396,2	MCF-7	breast:
6	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
7	chr19:39413074..39415034-chr19:39423613..39425226,2	K562	blood:
8	chr19:39422663..39425389-chr19:39427254..39430222,2	MCF-7	breast:
9	chr19:39424291..39427165-chr19:39431184..39433812,2	K562	blood:
10	chr19:39332856..39334895-chr19:39423283..39424833,2	MCF-7	breast:

No data

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

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10407879	0.86[ASN][1000 genomes]
rs10410176	0.86[ASN][1000 genomes]
rs1134180	0.86[ASN][1000 genomes]
rs2099339	0.83[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2116854	0.86[ASN][1000 genomes]
rs2116855	0.86[ASN][1000 genomes]
rs2288855	0.80[EUR][1000 genomes]
rs4801945	0.81[EUR][1000 genomes]
rs4803066	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803067	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6508825	LGALS14	cis	parietal	SCAN
rs6508825	C5AR1	cis	parietal	SCAN
rs6508825	PRR19	cis	parietal	SCAN
rs6508825	HNRNPUL1	cis	parietal	SCAN
rs6508825	PLD3	cis	parietal	SCAN
rs6508825	CEACAM4	cis	parietal	SCAN
rs6508825	NAPA	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:39422400-39434600	Weak transcription	Fetal Kidney	kidney
3	chr19:39422400-39435000	Weak transcription	Fetal Lung	lung
4	chr19:39422400-39435000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
6	chr19:39422600-39425200	Weak transcription	Primary B cells from cord blood	blood
7	chr19:39422600-39425200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:39422600-39425200	Weak transcription	Stomach Mucosa	stomach
9	chr19:39422600-39427000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:39422600-39430200	Weak transcription	HUVEC	blood vessel
11	chr19:39422600-39430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:39422600-39435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:39422600-39435200	Weak transcription	HSMM	muscle
14	chr19:39422600-39440200	Weak transcription	NH-A	brain
15	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
17	chr19:39422800-39424800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:39422800-39425200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:39422800-39425400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:39422800-39425600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:39422800-39432600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:39423000-39424800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39423000-39424800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:39423000-39424800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:39423000-39424800	Strong transcription	Brain Substantia Nigra	brain
26	chr19:39423000-39424800	Strong transcription	Fetal Thymus	thymus
27	chr19:39423000-39425200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:39423000-39425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:39423000-39425200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr19:39423000-39425400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr19:39423000-39425400	Strong transcription	Fetal Stomach	stomach
32	chr19:39423000-39425600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:39423000-39425800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39423000-39425800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr19:39423000-39425800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:39423000-39425800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr19:39423200-39424800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39423200-39424800	Strong transcription	NHEK	skin
39	chr19:39423200-39425000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39423200-39425200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:39423200-39425400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:39423200-39425400	Strong transcription	Placenta	Placenta
43	chr19:39423200-39425600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39423200-39425800	Strong transcription	Primary T cells from cord blood	blood
45	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
46	chr19:39423400-39424800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:39423400-39424800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:39423400-39424800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:39423400-39425400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:39423400-39425400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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