Variant report

Variant	rs1409134
Chromosome Location	chr10:90265464-90265465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90253538..90255456-chr10:90264130..90266420,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10509544	0.85[AMR][1000 genomes]
rs10736353	0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10736355	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10736357	0.82[AFR][1000 genomes]
rs10736358	0.80[AFR][1000 genomes]
rs10788597	0.81[CEU][hapmap]
rs10788601	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10788604	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788605	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887827	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887829	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177587	0.97[ASN][1000 genomes]
rs1183901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12266064	0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs12778446	0.80[CHB][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1325903	0.81[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1325907	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]
rs1359580	0.86[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs1952122	0.88[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2077890	1.00[ASN][1000 genomes]
rs2153856	0.88[ASW][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2437871	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[LWK][hapmap]
rs2437872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2437874	0.87[ASN][1000 genomes]
rs2437877	0.98[ASN][1000 genomes]
rs2437878	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]
rs2477952	0.85[CHB][hapmap]
rs2477955	0.96[ASN][1000 genomes]
rs2477957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2488271	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2576166	0.85[CHB][hapmap]
rs2576174	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs2576179	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2765442	0.87[ASN][1000 genomes]
rs2765444	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2986118	0.86[ASN][1000 genomes]
rs6586130	0.83[AMR][1000 genomes]
rs7075544	0.87[AFR][1000 genomes]
rs7077182	0.81[CEU][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7096710	0.88[ASW][hapmap];0.80[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs725683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs725684	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs745354	0.86[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs7895199	0.83[AMR][1000 genomes]
rs7902230	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907866	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7913372	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7917100	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7919420	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7922053	0.85[AMR][1000 genomes]

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	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	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
3	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1409134	RNLS	cis	cerebellum	SCAN
rs1409134	LIPM	cis	cerebellum	SCAN
rs1409134	BTAF1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90258200-90267200	Weak transcription	Adipose Nuclei	Adipose
2	chr10:90260400-90266600	Weak transcription	Fetal Lung	lung
3	chr10:90260400-90277600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr10:90263800-90265800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr10:90263800-90266200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr10:90264800-90266000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr10:90264800-90266000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr10:90264800-90266200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr10:90265000-90265600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:90265000-90266000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr10:90265000-90266200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr10:90265000-90266200	Enhancers	HUES6 Cell Line	embryonic stem cell

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