Variant report

Variant	rs12545826
Chromosome Location	chr8:9942907-9942908
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9911742..9913347-chr8:9941855..9944442,2	K562	blood:

Variant related genes	Relation type
ENSG00000260093	Chromatin interaction
ENSG00000175806	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10107485	0.84[JPT][hapmap]
rs11249968	0.84[ASN][1000 genomes]
rs11249969	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11249970	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1160369	0.82[CHB][hapmap]
rs11774411	0.86[CHB][hapmap]
rs11779614	0.80[ASN][1000 genomes]
rs11783851	0.86[CHB][hapmap];0.80[AMR][1000 genomes]
rs12542030	0.81[JPT][hapmap]
rs12545775	0.81[JPT][hapmap]
rs12545788	0.81[JPT][hapmap]
rs12547884	0.87[CHB][hapmap]
rs12549943	0.82[CHB][hapmap]
rs12550614	0.94[ASN][1000 genomes]
rs12679328	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12680389	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs13249013	0.82[CHB][hapmap]
rs13250499	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13256357	0.81[CHB][hapmap]
rs13261836	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13279619	0.94[ASN][1000 genomes]
rs1484645	0.82[CHB][hapmap]
rs1564808	0.81[CHB][hapmap]
rs17151190	0.82[CHB][hapmap]
rs17155393	0.81[JPT][hapmap]
rs2409632	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2898242	0.82[CHB][hapmap]
rs35349653	0.83[ASN][1000 genomes]
rs3735823	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4840462	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4841277	0.90[ASN][1000 genomes]
rs4841279	0.86[JPT][hapmap]
rs625218	0.95[JPT][hapmap]
rs685218	0.91[JPT][hapmap]
rs6981546	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6983566	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6997865	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7008407	0.81[CHB][hapmap]
rs7012221	0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs7831989	0.89[ASN][1000 genomes]
rs7832431	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs814421	0.82[ASN][1000 genomes]
rs814422	0.82[ASN][1000 genomes]
rs814424	0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs860068	0.83[ASN][1000 genomes]
rs9329215	0.82[CHB][hapmap]

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	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12545826	C8orf48	cis	cerebellum	SCAN
rs12545826	CLDN23	cis	multi-tissue	Pritchard
rs12545826	BLK	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9913200-9944800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:9914800-9947200	Weak transcription	Left Ventricle	heart
3	chr8:9929600-9947200	Weak transcription	Aorta	Aorta
4	chr8:9936200-9944200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:9938800-9944800	Weak transcription	Primary B cells from cord blood	blood
6	chr8:9940000-9949400	Weak transcription	Spleen	Spleen
7	chr8:9940200-9948600	Weak transcription	Primary T cells from cord blood	blood
8	chr8:9940600-9944200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr8:9941400-9944400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr8:9941600-9947200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:9941800-9944600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:9941800-9944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:9942000-9947200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:9942200-9944600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr8:9942200-9944800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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