Variant report

Variant	rs12299540
Chromosome Location	chr12:12354407-12354408
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	chr12:12353652..12355834-chr12:12365732..12367284,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10466849	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834671	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317629	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321417	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425946	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087862	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061128	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061156	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061161	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs12299540	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
3	chr12:12315400-12371600	Weak transcription	Lung	lung
4	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:12335200-12365800	Weak transcription	NHEK	skin
7	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
9	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
11	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
12	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:12338200-12355800	Weak transcription	Stomach Mucosa	stomach
14	chr12:12339200-12357600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:12340600-12359400	Weak transcription	Ovary	ovary
16	chr12:12342200-12360000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:12344000-12355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:12344000-12367800	Weak transcription	NHLF	lung
19	chr12:12344200-12355400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:12344200-12367200	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:12344200-12367400	Weak transcription	Brain Substantia Nigra	brain
22	chr12:12344200-12367800	Weak transcription	NH-A	brain
23	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
24	chr12:12347400-12355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:12347600-12367800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:12348800-12367000	Weak transcription	HUVEC	blood vessel
27	chr12:12349000-12367600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:12349600-12356000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:12349800-12354800	Weak transcription	HMEC	breast
30	chr12:12349800-12355800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:12350200-12356400	Weak transcription	Dnd41	blood
32	chr12:12351200-12354800	Strong transcription	Fetal Lung	lung
33	chr12:12351200-12355200	Weak transcription	Brain Germinal Matrix	brain
34	chr12:12351200-12356800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:12351400-12361800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:12351600-12356800	Weak transcription	Placenta	Placenta
37	chr12:12351800-12354800	Weak transcription	Fetal Thymus	thymus
38	chr12:12351800-12355600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr12:12351800-12360000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:12352000-12354600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:12352000-12355400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:12352000-12355600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr12:12352000-12355600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:12352000-12355800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:12352000-12356000	Strong transcription	HepG2	liver
46	chr12:12352000-12356200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:12352000-12356600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:12352200-12362000	Weak transcription	Brain Angular Gyrus	brain
49	chr12:12352200-12367200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:12352400-12355800	Strong transcription	A549	lung

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