Variant report

Variant	rs4308699
Chromosome Location	chr8:38979868-38979869
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10089487	0.86[MEX][hapmap];0.83[TSI][hapmap]
rs10958535	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10958537	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12542529	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12543388	0.82[AFR][1000 genomes]
rs12545085	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12548416	0.82[AFR][1000 genomes]
rs12549232	0.87[CHB][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13274715	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13280710	0.85[YRI][hapmap]
rs34002881	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34382496	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34494323	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35275553	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35335280	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35935390	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36042872	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236755	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236757	0.83[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4292654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4324895	0.83[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4419781	0.85[YRI][hapmap]
rs4495395	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4527834	0.85[YRI][hapmap]
rs4531014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4590405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4593506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4601278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[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]
rs4733975	0.85[YRI][hapmap]
rs4733979	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4733980	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4733981	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474108	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71517749	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7832578	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7838874	0.83[TSI][hapmap]
rs9650326	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021581	chr8:38934014-39043954	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1015907	chr8:38967169-39718559	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv539550	chr8:38967169-39718559	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4308699	TM2D2	cis	parietal	SCAN
rs4308699	DDHD2	cis	cerebellum	SCAN
rs4308699	ADAM32	cis	parietal	SCAN
rs4308699	TM2D2	cis	cerebellum	SCAN
rs4308699	ADAM32	cis	cerebellum	SCAN
rs4308699	RNF170	cis	cerebellum	SCAN
rs4308699	SGK196	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38971200-38981600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:38971200-38985400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:38971200-39036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:38978600-38989400	Weak transcription	Aorta	Aorta
5	chr8:38979200-39001000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links