Variant report

Variant	rs10845499
Chromosome Location	chr12:12407232-12407233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12406030..12408982-chr12:12413928..12415647,2	MCF-7	breast:
2	chr12:12369208..12371594-chr12:12405892..12408383,3	K562	blood:
3	chr12:12405750..12410285-chr12:12418275..12422138,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10083170	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	1.00[CHB][hapmap]
rs10845497	0.92[EUR][1000 genomes]
rs10845500	0.90[EUR][1000 genomes]
rs11054702	1.00[CEU][hapmap]
rs11054705	1.00[CEU][hapmap]
rs11054707	1.00[CEU][hapmap]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs11054767	1.00[JPT][hapmap]
rs11829211	0.83[EUR][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12297598	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12309246	1.00[CEU][hapmap]
rs12310020	1.00[JPT][hapmap]
rs12311922	0.92[EUR][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12317629	0.81[AMR][1000 genomes]
rs12319942	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321417	0.81[AMR][1000 genomes]
rs12422312	1.00[CHB][hapmap]
rs12425185	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12425699	1.00[CEU][hapmap]
rs12425946	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs12427198	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap]
rs16907789	1.00[CEU][hapmap]
rs28448423	0.92[EUR][1000 genomes]
rs56998126	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.87[EUR][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.85[EUR][1000 genomes]
rs74061123	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061156	0.81[AMR][1000 genomes]
rs7957531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.90[EUR][1000 genomes]
rs9630266	1.00[CEU][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10845499	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:12384800-12417200	Weak transcription	K562	blood
3	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
5	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
6	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:12392400-12407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:12392600-12408200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
11	chr12:12394600-12407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:12394800-12407600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:12395600-12409200	Weak transcription	Ovary	ovary
15	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:12396000-12407400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:12397000-12408400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:12397400-12409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:12397600-12407600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:12397600-12409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:12397600-12416600	Weak transcription	Fetal Stomach	stomach
22	chr12:12397800-12416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:12397800-12417200	Weak transcription	Brain Anterior Caudate	brain
24	chr12:12398200-12407400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:12401000-12408200	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:12401200-12408200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:12401200-12409200	Weak transcription	Right Atrium	heart
28	chr12:12401200-12418000	Weak transcription	Brain Substantia Nigra	brain
29	chr12:12402000-12407400	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:12402400-12417200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:12402800-12408000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:12403000-12408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:12403400-12407600	Weak transcription	A549	lung
34	chr12:12403600-12408200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:12405000-12416600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:12405200-12407600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:12405200-12409200	Weak transcription	Lung	lung
38	chr12:12405200-12416600	Weak transcription	Left Ventricle	heart
39	chr12:12405600-12408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:12405600-12417400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:12405800-12407600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:12406000-12408200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:12406000-12412600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:12406200-12411800	Weak transcription	Fetal Intestine Small	intestine
45	chr12:12406400-12416800	Weak transcription	Hela-S3	cervix
46	chr12:12406600-12408400	Enhancers	Brain Germinal Matrix	brain
47	chr12:12406800-12407600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:12406800-12409000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:12407000-12407400	Weak transcription	HepG2	liver
50	chr12:12407200-12407600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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