Variant report

Variant	rs11054729
Chromosome Location	chr12:12361577-12361578
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	chr12:12360154..12361666-chr12:12367455..12370218,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10083170	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs10845497	0.96[EUR][1000 genomes]
rs10845499	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]
rs10845500	0.87[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];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs11054767	1.00[JPT][hapmap]
rs11829211	0.83[EUR][1000 genomes]
rs11834671	0.80[AMR][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12297598	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12309246	1.00[CEU][hapmap]
rs12310020	1.00[JPT][hapmap]
rs12311922	0.96[EUR][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12319942	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	1.00[CHB][hapmap]
rs12425185	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12425699	1.00[CEU][hapmap]
rs12425946	1.00[CHB][hapmap]
rs12427198	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap]
rs16907789	1.00[CEU][hapmap]
rs28448423	0.96[EUR][1000 genomes]
rs56998126	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.90[EUR][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74061123	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9630266	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	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
rs11054729	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
2	chr12:12315400-12371600	Weak transcription	Lung	lung
3	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:12335200-12365800	Weak transcription	NHEK	skin
5	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
7	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
8	chr12:12344000-12367800	Weak transcription	NHLF	lung
9	chr12:12344200-12367200	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:12344200-12367400	Weak transcription	Brain Substantia Nigra	brain
11	chr12:12344200-12367800	Weak transcription	NH-A	brain
12	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
13	chr12:12347600-12367800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:12348800-12367000	Weak transcription	HUVEC	blood vessel
15	chr12:12349000-12367600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:12351400-12361800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:12352200-12362000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:12352200-12367200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:12352600-12364400	Weak transcription	HSMM	muscle
20	chr12:12352600-12367600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:12353200-12367400	Weak transcription	Fetal Kidney	kidney
22	chr12:12353400-12367000	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:12354600-12367800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:12354800-12370400	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:12355000-12367800	Weak transcription	Gastric	stomach
26	chr12:12355400-12367400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:12355400-12367600	Weak transcription	Osteobl	bone
28	chr12:12355400-12369400	Weak transcription	Adipose Nuclei	Adipose
29	chr12:12355600-12365800	Weak transcription	Fetal Intestine Small	intestine
30	chr12:12355600-12367600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:12355600-12367600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:12355600-12367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:12355600-12367800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:12355600-12367800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:12355600-12369800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:12355800-12361600	Weak transcription	Fetal Heart	heart
37	chr12:12355800-12361600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:12355800-12364000	Weak transcription	Psoas Muscle	Psoas
39	chr12:12355800-12367000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:12355800-12367400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:12355800-12367600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:12355800-12367800	Weak transcription	Primary T cells from cord blood	blood
43	chr12:12355800-12374200	Weak transcription	Fetal Intestine Large	intestine
44	chr12:12356000-12367600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:12356000-12368800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:12356000-12369000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:12356000-12370000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:12356200-12366800	Weak transcription	Fetal Lung	lung
49	chr12:12356200-12367400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:12356400-12367600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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