Variant report

Variant	rs2708438
Chromosome Location	chr12:40615432-40615433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:40615378-40615621	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:40615413-40615464	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40611277..40614132-chr12:40614284..40617171,2	K562	blood:

Variant related genes	Relation type
LRRK2	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10506148	0.95[CHB][hapmap];0.95[ASN][1000 genomes]
rs10784340	1.00[YRI][hapmap]
rs10877955	1.00[YRI][hapmap]
rs10877971	1.00[YRI][hapmap]
rs10878123	1.00[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10878208	0.83[JPT][hapmap]
rs11174831	1.00[YRI][hapmap]
rs11174928	1.00[ASW][hapmap]
rs11175103	1.00[ASW][hapmap]
rs11175256	0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11175332	0.95[JPT][hapmap]
rs11175371	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11175401	0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11175405	0.89[JPT][hapmap]
rs11175422	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11175540	0.82[ASN][1000 genomes]
rs11175558	0.95[JPT][hapmap]
rs11564115	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs1388593	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1388596	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1472117	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491924	1.00[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1491939	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491942	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17443199	0.89[JPT][hapmap]
rs17458613	1.00[YRI][hapmap]
rs17484286	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1817817	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1907630	0.96[ASN][1000 genomes]
rs1907631	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1907634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046931	0.90[JPT][hapmap]
rs2131088	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2172240	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2172241	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2201144	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638244	0.90[JPT][hapmap]
rs2638268	0.90[JPT][hapmap]
rs2638270	0.95[JPT][hapmap]
rs2638271	0.90[JPT][hapmap]
rs2708426	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2708436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708437	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708441	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2723260	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2723268	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2723269	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28365179	0.94[JPT][hapmap]
rs4473003	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs7134572	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs72644819	0.82[ASN][1000 genomes]
rs7310104	0.90[JPT][hapmap]
rs949640	1.00[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40610800-40616600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:40611000-40615600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:40611000-40618000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40611200-40615600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:40611200-40617400	Weak transcription	A549	lung
6	chr12:40613600-40615600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:40615200-40616000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:40615400-40615600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr12:40615400-40617400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr12:40615400-40618000	Active TSS	Primary hematopoietic stem cells	blood

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