Variant report

Variant	rs2437871
Chromosome Location	chr10:90278380-90278381
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10736357	0.94[ASN][1000 genomes]
rs10736358	0.94[ASN][1000 genomes]
rs10749586	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs10749587	0.84[AMR][1000 genomes]
rs10749588	0.85[AMR][1000 genomes]
rs10887829	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10887831	0.83[YRI][hapmap]
rs11202750	0.85[AMR][1000 genomes]
rs11202766	0.91[YRI][hapmap]
rs11202772	0.88[JPT][hapmap]
rs1177587	0.88[AMR][1000 genomes]
rs1183901	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs12219242	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs12249510	0.81[YRI][hapmap]
rs12357364	0.91[YRI][hapmap]
rs12413139	0.90[YRI][hapmap]
rs1325903	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs1325907	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]
rs1359580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1409134	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[LWK][hapmap]
rs1925937	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935578	0.92[MEX][hapmap];0.86[AMR][1000 genomes]
rs1952122	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs1980812	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077890	0.94[AMR][1000 genomes]
rs2437872	0.82[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes]
rs2437874	0.92[AMR][1000 genomes]
rs2437877	0.91[AMR][1000 genomes]
rs2437878	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]
rs2477952	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2477955	0.89[AMR][1000 genomes]
rs2477957	0.85[CHB][hapmap];0.90[AMR][1000 genomes]
rs2477958	0.80[ASW][hapmap];0.83[YRI][hapmap]
rs2488271	0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs2576164	0.80[ASW][hapmap];0.83[YRI][hapmap]
rs2576166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576174	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs2576179	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs2576180	0.84[CHB][hapmap];0.88[AMR][1000 genomes]
rs2765442	0.92[AMR][1000 genomes]
rs2765444	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2986118	0.92[AMR][1000 genomes]
rs4403718	0.85[AMR][1000 genomes]
rs7075544	0.99[ASN][1000 genomes]
rs725683	0.82[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes]
rs725684	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.94[AMR][1000 genomes]
rs745354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7901991	0.81[LWK][hapmap];0.81[YRI][hapmap]
rs7904229	0.88[AMR][1000 genomes]
rs7916937	0.85[AMR][1000 genomes]
rs7917100	0.81[CHB][hapmap]
rs9664314	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2437871	LIPM	cis	cerebellum	SCAN
rs2437871	CCNJ	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90269000-90279600	Weak transcription	Left Ventricle	heart
2	chr10:90274800-90279600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:90275400-90281200	Weak transcription	Ovary	ovary
4	chr10:90277600-90278800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links