Variant report

Variant	rs11639440
Chromosome Location	chr15:82571046-82571047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11073036	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs11630197	0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11631813	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11633000	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11854289	0.94[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11854483	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12324875	0.80[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1501367	0.93[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1566559	0.89[ASN][1000 genomes]
rs1566560	0.89[ASN][1000 genomes]
rs1566561	0.82[ASN][1000 genomes]
rs16973457	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1846908	0.89[ASN][1000 genomes]
rs1948742	0.80[ASN][1000 genomes]
rs1972460	0.80[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2016372	0.83[ASN][1000 genomes]
rs2047679	0.93[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2134046	0.83[JPT][hapmap]
rs2457497	0.89[JPT][hapmap]
rs2665103	0.87[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs28454949	0.92[ASN][1000 genomes]
rs28522807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28610286	0.82[ASN][1000 genomes]
rs3759800	0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs3902959	0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4238534	0.80[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4267268	0.81[ASN][1000 genomes]
rs4296215	0.80[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4778674	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778986	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4778987	0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4778990	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56398167	0.81[ASN][1000 genomes]
rs61554133	0.87[ASN][1000 genomes]
rs62012055	0.80[ASN][1000 genomes]
rs7167504	0.80[ASN][1000 genomes]
rs7176926	0.91[ASN][1000 genomes]
rs72749557	0.80[ASN][1000 genomes]
rs72749560	0.80[ASN][1000 genomes]
rs72749561	0.80[ASN][1000 genomes]
rs72749564	0.81[ASN][1000 genomes]
rs72749586	0.83[ASN][1000 genomes]
rs7403041	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7403244	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025964	0.81[ASN][1000 genomes]
rs8027301	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs8027661	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs8030250	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs8033313	0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs905450	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9972440	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv904441	chr15:82532963-82580736	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv904442	chr15:82540174-82571046	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1054025	chr15:82540486-83058214	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv904443	chr15:82553472-82571780	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11639440	FAM154B	cis	cerebellum	SCAN
rs11639440	RASGRF1	cis	cerebellum	SCAN
rs11639440	FAM154B	cis	parietal	SCAN
rs11639440	AP3B2	cis	parietal	SCAN
rs11639440	AP3B2	cis	cerebellum	SCAN
rs11639440	EFTUD1	cis	parietal	SCAN
rs11639440	CPEB1	cis	parietal	SCAN

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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