Variant report

Variant	rs9845388
Chromosome Location	chr3:158137884-158137885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11707696	0.93[EUR][1000 genomes]
rs11719388	0.94[EUR][1000 genomes]
rs60745172	0.80[ASN][1000 genomes]
rs73168795	0.94[EUR][1000 genomes]
rs7617666	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621889	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1000904	chr3:158094357-158159317	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9845388	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs9845388	RP11-538P18.2	cis	Adipose Subcutaneous	GTEx
rs9845388	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158124600-158146600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:158136600-158138800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:158137200-158138200	Enhancers	GM12878-XiMat	blood
4	chr3:158137200-158139800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:158137400-158138200	Enhancers	Stomach Mucosa	stomach
6	chr3:158137400-158139600	Enhancers	NHEK	skin
7	chr3:158137600-158138200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:158137600-158138200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr3:158137600-158139000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:158137600-158139400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:158137600-158139400	Enhancers	HMEC	breast
12	chr3:158137600-158139600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:158137800-158138000	Enhancers	Esophagus	oesophagus
14	chr3:158137800-158138000	Enhancers	Small Intestine	intestine
15	chr3:158137800-158139600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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