Variant report

Variant	rs1750274
Chromosome Location	chr10:90225923-90225924
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10509552	0.82[JPT][hapmap]
rs1067839	0.96[CEU][hapmap];0.94[AMR][1000 genomes]
rs1067840	0.96[CEU][hapmap];0.94[AMR][1000 genomes]
rs10736351	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10736352	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10736354	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10749589	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10749590	0.86[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10749591	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788598	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10788599	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10788600	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10788602	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10887817	0.85[CEU][hapmap]
rs10887818	0.85[CEU][hapmap]
rs10887821	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10887823	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10887824	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1169043	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1342450	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1342451	0.85[CEU][hapmap]
rs1342456	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1578696	0.91[CHB][hapmap]
rs1617881	0.85[CEU][hapmap]
rs1935579	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1935581	0.91[CHB][hapmap]
rs1935582	0.91[CHB][hapmap]
rs1935584	0.93[AMR][1000 genomes]
rs2096194	0.95[CEU][hapmap];0.80[CHB][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2185786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2209553	0.81[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs2312610	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2433340	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs2437875	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2477954	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477956	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576159	0.86[JPT][hapmap]
rs2576169	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576170	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576171	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576172	0.87[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576176	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2576181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2765454	0.81[AMR][1000 genomes]
rs2765456	0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs2872092	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4509673	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4596981	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4606392	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4619060	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4934403	0.85[CEU][hapmap]
rs4934404	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4934409	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4934411	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6586132	0.96[CEU][hapmap]
rs6586134	0.85[CEU][hapmap]
rs6586139	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7899828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7909697	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7910594	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7911996	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7918921	0.85[CEU][hapmap]
rs7921352	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs792205	0.85[CEU][hapmap]
rs792207	0.85[CEU][hapmap]
rs792208	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs792209	0.84[CEU][hapmap]
rs792211	0.93[AMR][1000 genomes]
rs792213	0.85[CEU][hapmap]
rs792214	0.92[CEU][hapmap];0.93[AMR][1000 genomes]
rs792215	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs792230	0.85[CEU][hapmap]
rs792234	0.84[CEU][hapmap]
rs792235	0.96[CEU][hapmap];0.93[AMR][1000 genomes]
rs7922551	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs796945	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs806694	0.96[CEU][hapmap];0.93[AMR][1000 genomes]
rs813782	0.96[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes]
rs814242	0.93[AMR][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	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1750274	LIPA	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90193800-90227600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:90216800-90227400	Weak transcription	Ovary	ovary
3	chr10:90218400-90226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:90220200-90226800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:90221000-90227400	Weak transcription	Right Atrium	heart
6	chr10:90221000-90227400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:90224200-90227400	Weak transcription	Right Ventricle	heart
8	chr10:90224800-90227400	Weak transcription	Left Ventricle	heart
9	chr10:90225200-90226000	Enhancers	Psoas Muscle	Psoas
10	chr10:90225600-90226400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:90225600-90227800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:90225800-90226400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:90225800-90228600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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