Variant report

Variant	rs512926
Chromosome Location	chr11:64437375-64437376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64436169..64437853-chr11:64450715..64453219,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10466694	1.00[EUR][1000 genomes]
rs10751010	1.00[MEX][hapmap]
rs10751011	1.00[MEX][hapmap]
rs11231806	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11231811	1.00[EUR][1000 genomes]
rs11231812	1.00[EUR][1000 genomes]
rs11231865	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11231866	1.00[EUR][1000 genomes]
rs11231892	1.00[MEX][hapmap]
rs11821081	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1212539	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs1212851	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs12273948	1.00[EUR][1000 genomes]
rs12280878	1.00[TSI][hapmap]
rs12281931	1.00[EUR][1000 genomes]
rs12293573	1.00[EUR][1000 genomes]
rs12294207	1.00[MEX][hapmap]
rs17146100	1.00[EUR][1000 genomes]
rs17146110	1.00[EUR][1000 genomes]
rs17146119	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs17159320	1.00[MEX][hapmap]
rs17159321	1.00[MEX][hapmap]
rs1787671	1.00[EUR][1000 genomes]
rs2022048	1.00[TSI][hapmap]
rs2022049	1.00[EUR][1000 genomes]
rs240690	1.00[MEX][hapmap]
rs2518908	1.00[EUR][1000 genomes]
rs2666561	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2666562	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs2904961	1.00[EUR][1000 genomes]
rs2959651	1.00[EUR][1000 genomes]
rs3016758	1.00[EUR][1000 genomes]
rs3016759	0.92[YRI][hapmap]
rs41323046	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs475704	0.91[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs516041	1.00[EUR][1000 genomes]
rs519106	1.00[MEX][hapmap]
rs534052	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs534073	1.00[EUR][1000 genomes]
rs535606	0.91[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs541305	1.00[EUR][1000 genomes]
rs545167	1.00[EUR][1000 genomes]
rs545819	0.91[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs546323	1.00[EUR][1000 genomes]
rs547280	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs550930	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs553618	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs559095	1.00[EUR][1000 genomes]
rs559977	1.00[EUR][1000 genomes]
rs56186064	1.00[EUR][1000 genomes]
rs565688	1.00[EUR][1000 genomes]
rs573545	0.91[ASW][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs57371796	1.00[EUR][1000 genomes]
rs579175	1.00[EUR][1000 genomes]
rs58571986	1.00[EUR][1000 genomes]
rs6591863	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7110778	1.00[EUR][1000 genomes]
rs7113097	1.00[EUR][1000 genomes]
rs7123003	1.00[MEX][hapmap]
rs7127435	1.00[EUR][1000 genomes]
rs73492139	1.00[EUR][1000 genomes]
rs73492140	1.00[EUR][1000 genomes]
rs73492144	1.00[EUR][1000 genomes]
rs73494206	1.00[EUR][1000 genomes]
rs7927181	1.00[TSI][hapmap]
rs7948607	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs7948832	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9326433	1.00[EUR][1000 genomes]
rs9326434	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9666331	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9666856	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
9	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
10	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
11	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
13	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs512926	SF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64421200-64453800	Weak transcription	Fetal Brain Male	brain
2	chr11:64428800-64440400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:64428800-64442600	Weak transcription	Right Atrium	heart
4	chr11:64428800-64442800	Weak transcription	Aorta	Aorta
5	chr11:64429400-64439600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:64429400-64442800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:64431600-64442000	Weak transcription	Brain Anterior Caudate	brain
8	chr11:64433000-64438800	Strong transcription	Brain Germinal Matrix	brain
9	chr11:64433600-64443200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:64434400-64438800	Strong transcription	Fetal Brain Female	brain
11	chr11:64435400-64437600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:64435800-64438000	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:64436000-64440600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:64436200-64439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:64436200-64440200	Weak transcription	Brain Angular Gyrus	brain
16	chr11:64436400-64438800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:64436400-64442600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:64436600-64442000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr11:64436600-64442400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:64436800-64437400	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr11:64436800-64437600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr11:64436800-64437600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:64436800-64437800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr11:64436800-64439800	Enhancers	Spleen	Spleen
25	chr11:64437000-64437600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr11:64437000-64437600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:64437200-64437800	Enhancers	K562	blood
28	chr11:64437200-64438800	Enhancers	Adipose Nuclei	Adipose
29	chr11:64437200-64439200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links