Variant report

Variant	rs1404998
Chromosome Location	chr7:39159402-39159403
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39155263..39157100-chr7:39158946..39161624,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11760350	0.80[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11761291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11761599	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11767715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11770808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap]
rs12056218	0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs1358003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16870180	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17171546	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2103194	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28718047	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4442034	0.88[TSI][hapmap]
rs61550119	0.81[EUR][1000 genomes]
rs62442189	0.81[EUR][1000 genomes]
rs62442206	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62442233	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62442235	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62442236	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62442237	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62443960	0.84[EUR][1000 genomes]
rs62443961	0.82[EUR][1000 genomes]
rs73126408	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73126409	0.82[EUR][1000 genomes]
rs8180838	0.93[CEU][hapmap];0.92[EUR][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	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv887968	chr7:39123165-39198960	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv830968	chr7:39127531-39283543	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv428163	chr7:39127531-39283543	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1404998	G3BP1	trans	parietal	SCAN
rs1404998	CDK13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39153200-39165800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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