Variant report

Variant	rs10077253
Chromosome Location	chr5:114694891-114694892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10036686	0.91[EUR][1000 genomes]
rs10052230	0.91[EUR][1000 genomes]
rs10052335	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10054091	0.91[EUR][1000 genomes]
rs10057172	1.00[JPT][hapmap]
rs10068248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072589	0.91[EUR][1000 genomes]
rs10078844	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10085045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477528	0.84[EUR][1000 genomes]
rs10478229	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10478230	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10478231	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1109015	0.95[EUR][1000 genomes]
rs1109016	0.95[EUR][1000 genomes]
rs12332367	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2004680	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2605185	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs269502	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2963764	1.00[ASN][1000 genomes]
rs3752050	0.85[CEU][hapmap]
rs3752051	0.85[CEU][hapmap]
rs3752052	0.85[CEU][hapmap]
rs3885971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749760	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713623	0.91[EUR][1000 genomes]
rs7713947	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs9986244	0.91[EUR][1000 genomes]
rs9986246	0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10077253	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114685600-114695800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:114690400-114695800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:114690800-114701400	Weak transcription	Hela-S3	cervix
4	chr5:114691200-114696000	Weak transcription	A549	lung
5	chr5:114691800-114695400	Weak transcription	Stomach Mucosa	stomach
6	chr5:114694000-114697000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:114694400-114696200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:114694400-114696600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:114694600-114695000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:114694600-114695200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr5:114694800-114695400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:114694800-114695600	Weak transcription	H1 Cell Line	embryonic stem cell

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