Variant report

Variant	rs2620472
Chromosome Location	chr7:147023864-147023865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10228191	0.82[JPT][hapmap]
rs10239550	0.82[JPT][hapmap]
rs10264424	0.82[JPT][hapmap]
rs10265626	0.82[JPT][hapmap]
rs1304809	0.91[JPT][hapmap]
rs13230403	0.86[JPT][hapmap]
rs1479841	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1479842	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1585815	0.91[JPT][hapmap]
rs1842275	0.82[JPT][hapmap]
rs2620475	0.82[JPT][hapmap]
rs2692131	0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs2692132	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2692133	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap]
rs2697452	0.91[JPT][hapmap]
rs2697453	0.82[JPT][hapmap]
rs2697457	0.91[JPT][hapmap]
rs28546178	0.88[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap]
rs6464815	0.81[JPT][hapmap]
rs6954639	0.96[YRI][hapmap]
rs700293	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs700296	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs700299	0.82[JPT][hapmap]
rs700300	0.82[JPT][hapmap]
rs700301	0.82[JPT][hapmap]
rs700306	0.82[JPT][hapmap]
rs700308	0.82[CHD][hapmap]
rs700311	0.91[JPT][hapmap]
rs826641	0.80[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs826645	0.91[JPT][hapmap]
rs826647	0.82[JPT][hapmap]
rs826649	0.80[JPT][hapmap]
rs826650	0.82[JPT][hapmap]
rs826651	0.82[JPT][hapmap]
rs826652	0.82[JPT][hapmap]
rs826655	0.82[JPT][hapmap]
rs826656	0.91[JPT][hapmap]
rs826657	0.91[JPT][hapmap]
rs826658	0.91[JPT][hapmap]
rs826659	0.91[JPT][hapmap]
rs826660	0.91[JPT][hapmap]
rs826661	0.90[JPT][hapmap]
rs826786	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs826788	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs826790	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs826793	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs826802	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826803	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs826812	0.91[JPT][hapmap]
rs826813	0.82[JPT][hapmap]
rs826814	0.82[JPT][hapmap]
rs826823	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs872713	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933033	chr7:146720301-147081560	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1033898	chr7:146721499-147081768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv931005	chr7:146730472-147381257	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv889396	chr7:146854133-147035067	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1033398	chr7:146989035-147101573	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
6	nsv465192	chr7:147001077-147086045	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
7	nsv608943	chr7:147001077-147086045	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
8	nsv526693	chr7:147011388-147054250	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv1018715	chr7:147012067-147052280	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv608953	chr7:147021553-147040881	Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2620472	LRRC61	cis	cerebellum	SCAN

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

No data

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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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