Variant report

Variant	rs2437878
Chromosome Location	chr10:90229234-90229235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10749586	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10749587	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10749588	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788604	0.96[ASN][1000 genomes]
rs10788605	0.96[ASN][1000 genomes]
rs10887827	0.96[ASN][1000 genomes]
rs10887829	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.96[ASN][1000 genomes]
rs11202750	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1177587	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1183901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12778446	0.80[CHB][hapmap]
rs1325903	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[LWK][hapmap]
rs1325907	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]
rs1359580	0.86[CHB][hapmap]
rs1409134	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.96[ASN][1000 genomes]
rs1925937	0.88[AMR][1000 genomes]
rs1935578	0.86[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1952122	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[LWK][hapmap]
rs1980812	0.88[AMR][1000 genomes]
rs2077890	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153856	0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap];0.86[ASN][1000 genomes]
rs2437871	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.88[AMR][1000 genomes]
rs2437872	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2437874	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2437877	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477952	0.85[CHB][hapmap];0.87[AMR][1000 genomes]
rs2477955	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2477957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488271	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576166	0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs2576174	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576179	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2576180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2765442	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765444	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2986118	0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4403718	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs725683	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs725684	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745354	0.86[CHB][hapmap]
rs7901991	0.83[LWK][hapmap]
rs7902230	0.96[ASN][1000 genomes]
rs7904229	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7916937	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7917100	0.95[CHB][hapmap];1.00[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2437878	LIPM	cis	cerebellum	SCAN
rs2437878	CCNJ	trans	cerebellum	SCAN
rs2437878	IFIT3	cis	parietal	SCAN
rs2437878	LIPA	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90227600-90237000	Weak transcription	Left Ventricle	heart
2	chr10:90228200-90234000	Weak transcription	Ovary	ovary
3	chr10:90228200-90234200	Weak transcription	Aorta	Aorta
4	chr10:90228400-90233000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:90228600-90232000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:90228600-90232400	Weak transcription	HMEC	breast
7	chr10:90228600-90234000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:90228800-90234000	Weak transcription	Hela-S3	cervix
9	chr10:90229200-90229400	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links