Variant report

Variant	rs1325907
Chromosome Location	chr10:90237398-90237399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10749586	0.93[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes]
rs10749587	0.92[AMR][1000 genomes]
rs10749588	0.93[AMR][1000 genomes]
rs10788604	0.94[ASN][1000 genomes]
rs10788605	1.00[ASN][1000 genomes]
rs10887827	1.00[ASN][1000 genomes]
rs10887829	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];1.00[ASN][1000 genomes]
rs11202750	0.85[CEU][hapmap];0.93[AMR][1000 genomes]
rs1177587	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1183901	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12778446	0.80[CHB][hapmap]
rs1325903	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[LWK][hapmap]
rs1359580	0.86[CHB][hapmap]
rs1409134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs1925937	0.91[AMR][1000 genomes]
rs1935578	0.86[ASW][hapmap];0.81[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes]
rs1952122	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[LWK][hapmap]
rs1980812	0.91[AMR][1000 genomes]
rs2077890	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153856	0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap];0.85[ASN][1000 genomes]
rs2437871	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[AMR][1000 genomes]
rs2437872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2437874	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2437877	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2437878	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477952	0.85[CHB][hapmap];0.90[AMR][1000 genomes]
rs2477955	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477957	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488271	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576166	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes]
rs2576174	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576180	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765442	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986118	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4403718	0.93[AMR][1000 genomes]
rs725683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745354	0.86[CHB][hapmap]
rs7901991	0.83[LWK][hapmap]
rs7902230	1.00[ASN][1000 genomes]
rs7904229	0.92[AMR][1000 genomes]
rs7916937	0.84[CEU][hapmap];0.93[AMR][1000 genomes]
rs7917100	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1325907	LIPA	cis	cerebellum	SCAN
rs1325907	IFIT3	cis	parietal	SCAN
rs1325907	CCNJ	trans	cerebellum	SCAN
rs1325907	LIPM	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90233800-90239200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr10:90234400-90238200	Weak transcription	Right Ventricle	heart
3	chr10:90235000-90240400	Weak transcription	Aorta	Aorta
4	chr10:90235400-90237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:90235400-90237800	Weak transcription	Fetal Heart	heart
6	chr10:90235400-90238200	Weak transcription	HSMM	muscle
7	chr10:90235600-90238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:90235600-90238800	Weak transcription	Ovary	ovary
9	chr10:90236400-90238600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr10:90237000-90238000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:90237000-90238400	Enhancers	Psoas Muscle	Psoas
12	chr10:90237000-90238600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr10:90237000-90239200	Enhancers	HMEC	breast
14	chr10:90237200-90237400	Enhancers	Left Ventricle	heart
15	chr10:90237200-90237800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:90237200-90238400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:90237200-90239000	Enhancers	NHEK	skin

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