Variant report

Variant	rs6987861
Chromosome Location	chr8:65709467-65709468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10098783	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10112945	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10283033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10808739	0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs10957319	0.91[CHB][hapmap]
rs10957322	0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10957323	0.85[EUR][1000 genomes]
rs10957324	0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11984829	0.83[TSI][hapmap]
rs11992601	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11992694	0.83[TSI][hapmap]
rs11996540	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs12156417	0.85[EUR][1000 genomes]
rs13258167	0.83[TSI][hapmap]
rs13265280	0.85[EUR][1000 genomes]
rs13271194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13271746	0.84[EUR][1000 genomes]
rs13272719	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs16931350	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs16931360	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2356985	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2356986	0.93[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2884073	0.81[TSI][hapmap]
rs2884074	0.93[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34338127	0.88[EUR][1000 genomes]
rs34520115	0.85[EUR][1000 genomes]
rs34781030	0.83[EUR][1000 genomes]
rs34782690	0.85[EUR][1000 genomes]
rs34896430	0.84[EUR][1000 genomes]
rs35196908	0.84[EUR][1000 genomes]
rs35328846	0.83[EUR][1000 genomes]
rs35407243	0.81[EUR][1000 genomes]
rs35926758	0.81[EUR][1000 genomes]
rs35928023	0.81[EUR][1000 genomes]
rs3824188	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4134342	0.85[EUR][1000 genomes]
rs4236936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4258041	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4269577	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4385495	1.00[ASW][hapmap];0.83[TSI][hapmap]
rs4392942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4397440	0.91[CHB][hapmap]
rs4472561	0.88[ASN][1000 genomes]
rs4480156	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4527914	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4549812	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4629907	0.85[EUR][1000 genomes]
rs4737199	0.83[EUR][1000 genomes]
rs4737678	0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs4737680	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4737681	1.00[ASW][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4737682	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4737683	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs55650602	0.85[EUR][1000 genomes]
rs55666601	0.85[EUR][1000 genomes]
rs55863909	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs55873211	0.85[EUR][1000 genomes]
rs57755888	0.84[EUR][1000 genomes]
rs58195923	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs58950093	0.85[EUR][1000 genomes]
rs58994922	0.83[EUR][1000 genomes]
rs61028788	0.83[EUR][1000 genomes]
rs62521118	0.83[EUR][1000 genomes]
rs62521129	0.84[EUR][1000 genomes]
rs62521148	0.85[EUR][1000 genomes]
rs6472151	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6472152	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs6472153	0.83[EUR][1000 genomes]
rs6472154	0.90[ASN][1000 genomes]
rs6997149	0.88[EUR][1000 genomes]
rs7009078	0.83[TSI][hapmap]
rs7462059	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7812644	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7814191	0.91[ASN][1000 genomes]
rs7814652	0.84[EUR][1000 genomes]
rs7821085	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7826214	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7826501	0.85[EUR][1000 genomes]
rs7829301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7831851	0.87[YRI][hapmap]
rs7842113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9918790	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534001	chr8:64992196-65798776	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	esv2761434	chr8:65578467-66567678	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6987861	USP9Y	trans	lymphoblastoid	seeQTL
rs6987861	KDM5D	trans	lymphoblastoid	seeQTL
rs6987861	RPS4Y1	trans	lymphoblastoid	seeQTL
rs6987861	EIF1AY	trans	lymphoblastoid	seeQTL
rs6987861	DDX3Y	trans	lymphoblastoid	seeQTL
rs6987861	CYP7B1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:65694800-65709800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr8:65699800-65709600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr8:65700000-65710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:65701200-65709600	Weak transcription	Ovary	ovary
5	chr8:65706200-65710600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:65707600-65712000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:65708000-65709600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr8:65708400-65709600	Weak transcription	Esophagus	oesophagus
9	chr8:65708400-65709600	Weak transcription	Pancreas	Pancrea
10	chr8:65709200-65709800	Enhancers	Liver	Liver
11	chr8:65709400-65709600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:65709400-65709600	Enhancers	Brain Anterior Caudate	brain
13	chr8:65709400-65709600	Enhancers	Brain Hippocampus Middle	brain
14	chr8:65709400-65709600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr8:65709400-65709600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:65709400-65709600	Enhancers	Fetal Brain Female	brain
17	chr8:65709400-65710000	Enhancers	Primary hematopoietic stem cells	blood
18	chr8:65709400-65710200	Enhancers	Fetal Brain Male	brain
19	chr8:65709400-65710200	Enhancers	Fetal Lung	lung
20	chr8:65709400-65710200	Enhancers	Right Ventricle	heart
21	chr8:65709400-65711400	Active TSS	GM12878-XiMat	blood

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