Variant report

Variant	rs1681464
Chromosome Location	chr11:104012656-104012657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10750684	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10750685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10791675	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs1483500	0.88[ASN][1000 genomes]
rs2128806	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2170719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361268	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs361269	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs361270	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs361273	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs361293	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs361300	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs361301	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809021	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs4755010	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs551198	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs551300	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs667801	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7123807	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7936429	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7946884	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760322	chr11:103760085-104374141	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1051448	chr11:103864766-104274112	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv541157	chr11:103864766-104274112	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1043976	chr11:103881236-104526403	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1040367	chr11:103956747-104440470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
6	esv1834487	chr11:103959760-104026977	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv430426	chr11:103978540-104099790	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1681464	PDGFD	cis	parietal	SCAN
rs1681464	CNTN5	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:103997000-104013400	Weak transcription	Ovary	ovary
2	chr11:104005800-104019400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:104005800-104031000	Weak transcription	Aorta	Aorta
4	chr11:104006200-104013400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:104008000-104017400	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links