Variant report

Variant	rs4779649
Chromosome Location	chr15:34088272-34088273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10519873	1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs10519874	1.00[CHB][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs10519875	1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs11072659	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11852447	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11853406	0.89[EUR][1000 genomes]
rs11857110	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12438127	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901888	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906961	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908009	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1429752	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1429753	0.85[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1594252	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1594253	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864335	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864337	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2082075	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2163141	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288609	0.85[CHD][hapmap]
rs34424248	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35477217	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145827	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs735612	1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs7402430	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037952	0.97[ASN][1000 genomes]
rs8038562	0.85[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8042318	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042469	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042964	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs965471	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv568921	chr15:34046635-34247622	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1044844	chr15:34065524-34296829	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4779649	PGBD4	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34051000-34089200	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:34061600-34121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:34071400-34107200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:34073800-34102800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:34078600-34099000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:34080800-34105000	Weak transcription	Aorta	Aorta
7	chr15:34081000-34093800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:34081000-34094200	Weak transcription	Brain Anterior Caudate	brain
9	chr15:34081000-34094200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:34081000-34102400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:34081600-34088400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:34082000-34090800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:34084600-34095600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:34087400-34089400	Weak transcription	Fetal Lung	lung
15	chr15:34087400-34093200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:34087600-34094200	Weak transcription	Fetal Stomach	stomach

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