Variant report

Variant	rs878010
Chromosome Location	chr12:40502645-40502646
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40404217..40405558-chr12:40500388..40503110,15	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1031996	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748014	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10784359	0.90[MEX][hapmap]
rs10784370	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10784381	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10878089	0.90[MEX][hapmap]
rs10878113	0.83[EUR][1000 genomes]
rs10878222	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10878224	0.84[CHB][hapmap]
rs1117378	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175024	0.90[MEX][hapmap]
rs11175275	0.90[EUR][1000 genomes]
rs11175326	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11175327	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11175656	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12230710	0.82[EUR][1000 genomes]
rs1352876	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1388589	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1388590	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1388591	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1463719	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs1463720	0.87[ASN][1000 genomes]
rs1472118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1482284	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1482285	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1482287	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1482288	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1491927	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1491929	0.84[ASN][1000 genomes]
rs1491930	0.82[ASN][1000 genomes]
rs1491931	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1844921	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1844922	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1873612	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1905121	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1948380	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2131082	0.84[ASN][1000 genomes]
rs2131083	0.84[ASN][1000 genomes]
rs2170503	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2201143	0.84[ASN][1000 genomes]
rs2220677	0.84[ASN][1000 genomes]
rs2248928	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs2249010	0.89[JPT][hapmap]
rs2249017	0.89[JPT][hapmap]
rs2404573	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638231	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638232	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638245	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638249	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638251	0.82[ASN][1000 genomes]
rs2638254	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638257	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638258	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638259	0.86[ASN][1000 genomes]
rs2638260	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638262	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638263	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638264	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638266	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638267	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2708449	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708464	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708466	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708467	0.84[ASN][1000 genomes]
rs2708470	0.84[ASN][1000 genomes]
rs2708472	0.84[ASN][1000 genomes]
rs2708473	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708474	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708476	0.82[ASN][1000 genomes]
rs2708477	0.89[JPT][hapmap]
rs2708479	0.89[JPT][hapmap]
rs2708480	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708481	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs2708485	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708488	0.82[ASN][1000 genomes]
rs2708491	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708492	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708493	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708494	0.85[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2896905	0.85[MEX][hapmap]
rs3812791	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4363681	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581514	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581519	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132203	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs716231	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs722817	0.82[ASN][1000 genomes]
rs728622	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs728623	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs729216	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7306140	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310430	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs900253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937109	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937110	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937111	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1846566	chr12:40498683-40527395	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv1838306	chr12:40499495-40527395	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs878010	LRRK2	cis	parietal	SCAN
rs878010	SLC2A13	cis	parietal	SCAN
rs878010	AC079630.2	cis	Esophagus Mucosa	GTEx
rs878010	LRRK2	cis	cerebellum	SCAN
rs878010	ZCRB1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40501200-40502800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:40501200-40510200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:40501600-40504200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:40501600-40504400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:40501600-40504400	Weak transcription	NHDF-Ad	bronchial
6	chr12:40502200-40503200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:40502600-40504200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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