Variant report

Variant	rs950690
Chromosome Location	chr3:109272484-109272485
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1528901	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544022	0.80[EUR][1000 genomes]
rs1609370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609371	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729603	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729608	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729610	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729614	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1729623	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1732173	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732191	0.80[EUR][1000 genomes]
rs1732216	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1732217	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1732219	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1732220	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1732222	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1732223	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2687274	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6437855	0.85[EUR][1000 genomes]
rs6437859	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6800450	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6803024	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs884245	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs884246	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9832660	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460814	chr3:109195046-109381428	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591268	chr3:109195046-109381428	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv470827	chr3:109195046-109433855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs950690	NLE1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109270600-109273400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:109270600-109273600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:109271200-109272600	Weak transcription	Dnd41	blood
4	chr3:109271400-109272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:109271400-109272600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:109271800-109273600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:109272000-109273600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:109272400-109272800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:109272400-109272800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:109272400-109273000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:109272400-109273000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:109272400-109273000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:109272400-109273600	Enhancers	Hela-S3	cervix
14	chr3:109272400-109273600	Enhancers	NH-A	brain

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