Variant report

Variant	rs9662660
Chromosome Location	chr1:221736879-221736880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DUSP10-2	chr1:221736650-221736978	XLOC_001212
2	lnc-DUSP10-2	chr1:221736650-221736994	NONHSAT009644

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1026515	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10495169	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118753	0.81[EUR][1000 genomes]
rs11118755	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118757	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11118759	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11118764	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118772	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11118774	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12021531	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025803	0.84[AMR][1000 genomes]
rs12026855	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12032922	0.82[CEU][hapmap]
rs12039969	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046891	0.84[AMR][1000 genomes]
rs12117680	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12127875	0.81[EUR][1000 genomes]
rs12142838	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12564947	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1338077	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1538249	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17010241	0.85[AMR][1000 genomes]
rs1933267	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4129174	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs953400	0.95[CEU][hapmap]
rs9658820	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9658836	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9725124	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1009838	chr1:221692621-221773945	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535301	chr1:221692621-221773945	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9662660	LYPLAL1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221729800-221748600	Weak transcription	Left Ventricle	heart
2	chr1:221729800-221748800	Weak transcription	Pancreas	Pancrea
3	chr1:221735400-221737400	Enhancers	Liver	Liver
4	chr1:221736600-221737000	Enhancers	Psoas Muscle	Psoas
5	chr1:221736600-221737200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:221736600-221737200	Enhancers	Ovary	ovary
7	chr1:221736600-221737200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr1:221736600-221737200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr1:221736800-221737000	Weak transcription	Right Atrium	heart
10	chr1:221736800-221737200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links