Variant report

Variant	rs17545254
Chromosome Location	chr19:39414834-39414835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39414056-39415761	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39414723-39415514	K562	blood:	n/a	n/a
3	POLR2A	chr19:39414791-39415029	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39334351..39336976-chr19:39412590..39415295,2	K562	blood:
2	chr19:39413074..39415034-chr19:39423613..39425226,2	K562	blood:
3	chr19:39341116..39343070-chr19:39413366..39415101,2	K562	blood:

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000269688	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10416055	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425217	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10775533	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083488	0.86[EUR][1000 genomes]
rs11083489	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668245	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610409	0.92[ASN][1000 genomes]
rs12972986	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979755	0.92[ASN][1000 genomes]
rs12985428	0.87[EUR][1000 genomes]
rs1808661	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1808662	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865047	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865049	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3136640	0.92[ASN][1000 genomes]
rs4801971	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802998	0.92[ASN][1000 genomes]
rs4803006	0.92[ASN][1000 genomes]
rs4803034	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257007	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730078	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508411	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508539	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113389	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9636109	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9749516	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17545254	CTC-360G5.9	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
3	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39395600-39415000	Weak transcription	Hela-S3	cervix
5	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
6	chr19:39398600-39415000	Weak transcription	Brain Substantia Nigra	brain
7	chr19:39398800-39415000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:39402800-39420200	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:39403000-39415000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:39403600-39420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:39403800-39420200	Weak transcription	Fetal Brain Male	brain
12	chr19:39406400-39420000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:39406800-39420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:39409000-39417400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:39409200-39419000	Strong transcription	Fetal Intestine Small	intestine
16	chr19:39409200-39420400	Weak transcription	Stomach Mucosa	stomach
17	chr19:39409600-39418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:39410000-39417400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:39410200-39417600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:39411200-39415000	Weak transcription	HSMM	muscle
21	chr19:39411400-39415000	Weak transcription	HUVEC	blood vessel
22	chr19:39411400-39419000	Strong transcription	Fetal Stomach	stomach
23	chr19:39411600-39417000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:39411600-39420400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:39411600-39420400	Weak transcription	Fetal Heart	heart
26	chr19:39411800-39417200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:39412000-39416600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:39412000-39417000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr19:39412000-39417200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:39412000-39417200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:39412000-39417600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:39412000-39419000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:39412000-39419600	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:39412200-39417000	Strong transcription	Right Ventricle	heart
35	chr19:39412200-39417400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr19:39412200-39419200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:39412400-39415600	Strong transcription	Pancreas	Pancrea
38	chr19:39412400-39416600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:39412400-39417200	Strong transcription	Fetal Intestine Large	intestine
40	chr19:39412600-39415000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:39412800-39420600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:39413000-39415000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:39413200-39415000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:39413200-39415000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr19:39413200-39415000	Weak transcription	Thymus	Thymus
46	chr19:39413200-39415200	Weak transcription	Brain Germinal Matrix	brain
47	chr19:39413200-39418800	Weak transcription	GM12878-XiMat	blood
48	chr19:39413200-39420200	Weak transcription	Primary B cells from cord blood	blood
49	chr19:39413200-39420200	Weak transcription	NH-A	brain
50	chr19:39413200-39420200	Weak transcription	NHLF	lung

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