Variant report

Variant	rs2708909
Chromosome Location	chr7:48051679-48051680
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10225968	0.81[TSI][hapmap]
rs10256256	0.85[TSI][hapmap]
rs10276338	0.82[EUR][1000 genomes]
rs10951942	0.83[TSI][hapmap]
rs11767002	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11772387	0.83[TSI][hapmap]
rs12535580	0.83[TSI][hapmap]
rs12702405	0.80[EUR][1000 genomes]
rs1318327	0.80[EUR][1000 genomes]
rs1574242	0.83[TSI][hapmap]
rs1915960	0.81[TSI][hapmap]
rs2140113	0.83[TSI][hapmap]
rs2348666	0.85[TSI][hapmap]
rs2686783	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2686795	0.87[ASW][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs2708851	0.96[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2708874	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2708883	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708884	0.88[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708885	0.94[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708891	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708901	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881991	0.83[TSI][hapmap]
rs6944437	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6962900	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7779252	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7791084	0.83[TSI][hapmap]
rs7807654	0.83[TSI][hapmap]
rs7807750	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2708909	UPP1	cis	cerebellum	SCAN
rs2708909	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2708909	HUS1	cis	cerebellum	SCAN
rs2708909	PKD1L1	cis	cerebellum	SCAN
rs2708909	PKD1L1	cis	parietal	SCAN
rs2708909	UPP1	cis	Muscle Skeletal	GTEx
rs2708909	ABCA13	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48050400-48051800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:48050400-48052000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:48050800-48052000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr7:48051000-48051800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr7:48051000-48052000	Enhancers	Rectal Smooth Muscle	rectum
6	chr7:48051200-48051800	Weak transcription	Fetal Lung	lung
7	chr7:48051200-48052000	Enhancers	Fetal Heart	heart
8	chr7:48051400-48051800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:48051400-48052000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr7:48051400-48052000	Enhancers	Primary B cells from peripheral blood	blood
11	chr7:48051600-48051800	Enhancers	GM12878-XiMat	blood

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