Variant report

Variant	rs158624
Chromosome Location	chr5:36865669-36865670
allele	A/C
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	chr5:36865373-36866688	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36856261..36858596-chr5:36864059..36865980,2	K562	blood:
2	chr5:36861592..36864864-chr5:36865418..36867970,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf42-2	chr5:36864527-36866128	ENSG00000248044

Variant related genes	Relation type
ENSG00000272103	TF binding region
ENSG00000272103	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12657771	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13158310	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13170811	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13180309	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466862	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs150380	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151944	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs158622	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158623	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158791	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158796	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158803	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159749	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159751	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159753	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs159755	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs159913	0.84[EUR][1000 genomes]
rs168662	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184182	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs186173	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs188488	0.82[AMR][1000 genomes]
rs188541	0.82[EUR][1000 genomes]
rs292182	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs292183	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs292184	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs292194	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs292195	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs296962	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs300053	0.81[EUR][1000 genomes]
rs300055	0.83[EUR][1000 genomes]
rs300058	0.84[EUR][1000 genomes]
rs300060	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300061	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300063	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300064	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs300065	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs301859	0.83[EUR][1000 genomes]
rs301901	0.83[EUR][1000 genomes]
rs301917	0.83[EUR][1000 genomes]
rs3104057	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs388098	0.83[EUR][1000 genomes]
rs6875748	0.84[EUR][1000 genomes]
rs6899155	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv532133	chr5:36834932-36906436	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs158624	LOC646719	cis	occipital cortex	BrainEAC
rs158624	LOC646719	cis	hippocampus	BrainEAC
rs158624	LOC646719	cis	cerebellar cortex	BrainEAC
rs158624	LOC646719	cis	temporal cortex	BrainEAC
rs158624	LOC646719	cis	frontal cortex	BrainEAC
rs158624	LOC646719	cis	thalamus	BrainEAC
rs158624	LOC646719	cis	brain	BrainEAC
rs158624	LOC646719	cis	intralobular white matter	BrainEAC

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36862400-36874000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:36862600-36873600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:36862600-36874800	Weak transcription	Aorta	Aorta
4	chr5:36862800-36873800	Weak transcription	NH-A	brain
5	chr5:36863000-36874800	Weak transcription	Left Ventricle	heart
6	chr5:36864000-36873400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:36864400-36873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:36864600-36871600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:36864600-36874000	Weak transcription	Fetal Stomach	stomach
10	chr5:36864600-36874000	Weak transcription	Thymus	Thymus
11	chr5:36864800-36873600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:36864800-36874000	Weak transcription	Fetal Intestine Small	intestine
13	chr5:36864800-36874800	Weak transcription	Placenta	Placenta
14	chr5:36865400-36871400	Weak transcription	Fetal Brain Female	brain
15	chr5:36865600-36867200	Weak transcription	Spleen	Spleen

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