Variant report

Variant	rs7403041
Chromosome Location	chr15:82580182-82580183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11073036	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs11630197	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11631813	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11633000	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639440	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[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];1.00[YRI][hapmap]
rs11854289	0.94[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11854483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12324875	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1501367	1.00[CHB][hapmap];0.94[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];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1846908	0.89[ASN][1000 genomes]
rs1948742	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs1972460	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2016372	0.83[ASN][1000 genomes]
rs2047679	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2134046	0.89[JPT][hapmap]
rs2457497	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2665103	0.93[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs28454949	0.92[ASN][1000 genomes]
rs28522807	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28610286	0.82[ASN][1000 genomes]
rs3759800	1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3902959	1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4238534	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4267268	0.81[ASN][1000 genomes]
rs4296215	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4778674	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778986	0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4778987	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4778990	0.95[AFR][1000 genomes];0.99[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]
rs7403244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025964	0.81[ASN][1000 genomes]
rs8027301	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8027661	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8030250	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs8033313	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs905450	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9972440	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7403041	CPEB1	cis	parietal	SCAN
rs7403041	EFTUD1	cis	parietal	SCAN
rs7403041	AP3B2	cis	cerebellum	SCAN
rs7403041	AP3B2	cis	parietal	SCAN
rs7403041	FAM154B	cis	parietal	SCAN
rs7403041	RASGRF1	cis	cerebellum	SCAN
rs7403041	FAM154B	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82576200-82580800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr15:82576400-82580600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr15:82576400-82580800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:82576400-82581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:82576600-82580400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr15:82577400-82580400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr15:82577600-82580400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:82578000-82580200	Enhancers	Primary B cells from peripheral blood	blood
9	chr15:82578400-82580200	Enhancers	Thymus	Thymus
10	chr15:82578600-82580400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr15:82579000-82580400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr15:82579800-82580400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:82579800-82580600	Enhancers	Primary T cells from cord blood	blood
14	chr15:82580000-82580200	Enhancers	GM12878-XiMat	blood
15	chr15:82580000-82580600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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