Variant report

Variant	rs1002599
Chromosome Location	chr1:158435250-158435251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10489833	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10489834	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10489835	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10797020	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10908650	0.97[ASN][1000 genomes]
rs10908656	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10908680	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11264989	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11264998	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11265002	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11265003	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1157525	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12041218	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12079889	0.84[ASN][1000 genomes]
rs12080815	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12081915	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12125929	0.92[ASN][1000 genomes]
rs12128525	0.99[ASN][1000 genomes]
rs12136056	0.86[ASN][1000 genomes]
rs12403393	0.96[ASN][1000 genomes]
rs12404821	0.99[ASN][1000 genomes]
rs12407049	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1342947	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1342958	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1418846	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1418847	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1573519	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs1873509	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1873510	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1873511	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1894040	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2157687	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2317969	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs34147968	0.99[ASN][1000 genomes]
rs35051889	0.95[ASN][1000 genomes]
rs4609418	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4657080	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs58380553	1.00[ASN][1000 genomes]
rs6697656	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs71517522	0.93[ASN][1000 genomes]
rs7512592	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7518808	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7549581	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs863345	0.85[CHB][hapmap]
rs863347	0.85[CHB][hapmap]
rs863351	0.85[CHB][hapmap]
rs863352	0.85[CHB][hapmap]
rs863365	0.85[CHB][hapmap]
rs950260	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs950487	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs952222	0.97[ASN][1000 genomes]
rs952223	0.97[ASN][1000 genomes]
rs952224	0.97[ASN][1000 genomes]
rs9651046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv998569	chr1:158317392-158443389	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv947133	chr1:158431706-158440282	Strong transcription Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1002599	CD5L	cis	parietal	SCAN
rs1002599	YY1AP1	cis	parietal	SCAN
rs1002599	KIRREL	cis	cerebellum	SCAN
rs1002599	CKS1B	cis	cerebellum	SCAN
rs1002599	DCST2	cis	cerebellum	SCAN
rs1002599	IGSF8	cis	cerebellum	SCAN
rs1002599	NUP210L	cis	cerebellum	SCAN
rs1002599	EFNA1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158431800-158435400	Weak transcription	Thymus	Thymus
2	chr1:158431800-158443200	Weak transcription	Fetal Thymus	thymus

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