Variant report

Variant	rs11743178
Chromosome Location	chr5:111642706-111642707
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10043705	0.94[CEU][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1004385	0.87[CHB][hapmap]
rs10052915	0.82[CHB][hapmap]
rs1019743	0.82[CHB][hapmap]
rs1019744	0.82[CHB][hapmap]
rs11749725	0.88[ASN][1000 genomes]
rs12519600	0.82[CHB][hapmap]
rs1464764	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1474360	0.81[CHB][hapmap]
rs1524426	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs17134325	0.93[ASN][1000 genomes]
rs1851888	0.85[ASN][1000 genomes]
rs2056585	0.83[CHB][hapmap]
rs2140625	0.82[CHB][hapmap]
rs2416283	0.82[CHB][hapmap]
rs2416284	0.82[CHB][hapmap]
rs60311998	0.84[ASN][1000 genomes]
rs61501911	0.84[ASN][1000 genomes]
rs6594584	0.85[ASN][1000 genomes]
rs6594585	0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs7445191	0.84[ASN][1000 genomes]
rs7706772	0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs821733	0.82[CHB][hapmap]
rs821734	0.88[CHB][hapmap]
rs821735	0.87[CHB][hapmap]
rs821745	0.82[CHB][hapmap]
rs821747	0.80[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1021530	chr5:111626266-111683317	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1028181	chr5:111628901-111683317	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11743178	PJA2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111635600-111651800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:111637400-111684600	Weak transcription	Aorta	Aorta
3	chr5:111638600-111643800	Enhancers	Fetal Heart	heart
4	chr5:111639800-111652400	Weak transcription	Left Ventricle	heart
5	chr5:111640000-111643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:111640000-111645600	Weak transcription	Right Atrium	heart
7	chr5:111640200-111656400	Weak transcription	Psoas Muscle	Psoas
8	chr5:111641400-111644200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:111642000-111643200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:111642200-111642800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr5:111642200-111643200	Enhancers	Fetal Brain Male	brain
12	chr5:111642200-111650800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:111642600-111642800	Enhancers	Brain Hippocampus Middle	brain

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