Variant report

Variant	rs2140113
Chromosome Location	chr7:48057656-48057657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10225968	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs10247913	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10253220	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10253238	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs10256256	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10261930	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10951937	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs10951938	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs10951940	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10951941	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10951942	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761275	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11762077	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11764799	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11766144	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11766891	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11767002	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11768277	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772387	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11772633	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11773348	0.88[EUR][1000 genomes]
rs12535580	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12537979	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12702405	0.87[CHB][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12702406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1318327	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13230023	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1574242	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1915960	0.89[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1915962	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1915965	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1915966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1915967	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915968	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915971	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915972	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037482	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348666	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2348667	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2348669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2348670	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2708883	0.81[TSI][hapmap]
rs2708909	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2881991	0.89[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2881992	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4332046	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4618593	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs6978838	0.92[CEU][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6979699	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7357251	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357327	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7456745	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7789930	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7791084	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7791572	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs7791823	0.97[EUR][1000 genomes]
rs7800590	0.87[AMR][1000 genomes]
rs7807611	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7807612	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7807654	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7807750	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7808462	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9690905	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2140113	PKD1L1	cis	cerebellum	SCAN
rs2140113	UPP1	cis	cerebellum	SCAN
rs2140113	UPP1	cis	multi-tissue	Pritchard
rs2140113	PKD1L1	cis	parietal	SCAN
rs2140113	ABCA13	cis	parietal	SCAN
rs2140113	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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