Variant report

Variant	rs439940
Chromosome Location	chr1:216347556-216347557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10495017	0.80[CHD][hapmap]
rs11120739	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs11120740	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs1115436	0.81[CHB][hapmap]
rs1324330	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs17026174	0.81[CHD][hapmap]
rs17026208	0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs17026219	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs1805049	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2034960	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2274117	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2669057	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs301736	0.81[CHB][hapmap]
rs301737	0.81[CHB][hapmap]
rs301742	0.81[CHB][hapmap]
rs301744	0.81[CHB][hapmap]
rs301745	0.81[CHB][hapmap]
rs301750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs301752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs301759	0.80[CHD][hapmap]
rs301760	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs301761	0.93[CEU][hapmap]
rs369731	0.81[CHB][hapmap]
rs3754064	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3767692	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs378340	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs385463	0.93[CEU][hapmap]
rs386654	0.93[CEU][hapmap];0.88[GIH][hapmap]
rs401269	0.82[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs404925	0.93[CEU][hapmap]
rs407590	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs415508	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap]
rs430652	0.81[CHB][hapmap]
rs4971260	0.93[ASN][1000 genomes]
rs588516	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs592642	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs600535	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs62906	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs646094	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs659875	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs669616	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs677648	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs680410	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap]
rs696719	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs700015	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs773498	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs9660965	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs9661602	0.93[CEU][hapmap];0.87[CHB][hapmap]

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	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv873176	chr1:216249570-216363137	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1006028	chr1:216268796-216432545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216345800-216347600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:216347000-216350000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:216347000-216356200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:216347200-216350400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:216347200-216350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:216347200-216350800	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links