Variant report

Variant	rs1729951
Chromosome Location	chr3:136500733-136500734
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136499197..136501261-chr3:136509704..136512204,2	K562	blood:
2	chr3:136489373..136491844-chr3:136498899..136501779,2	MCF-7	breast:
3	chr3:136498020..136500935-chr3:136501120..136504401,3	MCF-7	breast:
4	chr3:136470266..136473022-chr3:136498014..136500937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513014	0.93[CHB][hapmap];0.95[ASN][1000 genomes]
rs10935186	0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs11919030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12107125	0.87[ASN][1000 genomes]
rs12486911	1.00[YRI][hapmap]
rs12630999	0.87[JPT][hapmap]
rs1280622	0.91[EUR][1000 genomes]
rs1280624	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2062322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs28489907	0.85[ASN][1000 genomes]
rs35874192	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856637	0.87[JPT][hapmap]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4038587	0.93[CEU][hapmap]
rs4408829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4521165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs4678437	0.87[JPT][hapmap]
rs4678438	0.87[JPT][hapmap]
rs6439649	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs6439655	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6764567	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6789329	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6791142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6802702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6808312	0.87[JPT][hapmap]
rs7616204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7618518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs7618871	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs900818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs940174	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9825700	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9836231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9845762	0.87[JPT][hapmap]

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	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1729951	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs1729951	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136498000-136502800	Weak transcription	Hela-S3	cervix
2	chr3:136498200-136501000	Weak transcription	Spleen	Spleen
3	chr3:136498200-136502000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:136498200-136502400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:136498200-136502400	Weak transcription	A549	lung
6	chr3:136498200-136502600	Weak transcription	NH-A	brain
7	chr3:136498200-136504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:136498200-136505000	Weak transcription	Osteobl	bone
9	chr3:136498200-136505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:136498400-136502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:136498400-136502800	Weak transcription	HSMMtube	muscle
12	chr3:136498600-136502600	Weak transcription	HSMM	muscle
13	chr3:136499200-136502600	Weak transcription	Aorta	Aorta
14	chr3:136499200-136504400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:136499600-136502600	Weak transcription	Fetal Lung	lung
16	chr3:136500000-136505400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:136500200-136502400	Weak transcription	Fetal Stomach	stomach
18	chr3:136500200-136508000	Enhancers	Placenta	Placenta

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