Variant report

Variant	rs13149991
Chromosome Location	chr4:86520349-86520350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:86520202-86520539	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ARHGAP24	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10003669	0.84[ASN][1000 genomes]
rs11931290	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11937452	0.87[ASN][1000 genomes]
rs11943623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs11945515	0.85[ASN][1000 genomes]
rs12502332	0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs13103706	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs13106652	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs13108032	0.80[ASN][1000 genomes]
rs13123541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13129615	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131183	0.86[ASN][1000 genomes]
rs1482089	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1564559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2062100	0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2869361	0.92[ASN][1000 genomes]
rs4693120	0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4693711	0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4693712	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4693718	0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4693719	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4693720	0.82[ASN][1000 genomes]
rs6531839	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs6815397	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs6849280	0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7664042	0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs766570	0.94[ASN][1000 genomes]
rs7681100	0.82[ASN][1000 genomes]
rs7681661	0.82[ASN][1000 genomes]
rs7688899	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7694594	0.84[ASN][1000 genomes]
rs979337	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs9994722	0.87[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	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv829999	chr4:86500257-86666019	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13149991	PKD2	cis	cerebellum	SCAN
rs13149991	ARHGAP24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86487200-86521200	Weak transcription	HSMMtube	muscle
2	chr4:86513000-86522600	Weak transcription	Primary B cells from cord blood	blood
3	chr4:86517800-86542200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:86518000-86524400	Weak transcription	HSMM	muscle
5	chr4:86518600-86524800	Weak transcription	Fetal Heart	heart
6	chr4:86520200-86520400	Enhancers	Gastric	stomach
7	chr4:86520200-86520400	Enhancers	Left Ventricle	heart
8	chr4:86520200-86520400	Enhancers	Pancreas	Pancrea
9	chr4:86520200-86520600	Enhancers	Right Ventricle	heart
10	chr4:86520200-86520800	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:86520200-86521800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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