Variant report

Variant	rs58682800
Chromosome Location	chr12:12351294-12351295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10082834	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083170	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10466847	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10466848	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10845497	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845499	0.87[EUR][1000 genomes]
rs10845500	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054695	1.00[ASN][1000 genomes]
rs11054696	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054702	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054705	1.00[ASN][1000 genomes]
rs11054706	1.00[ASN][1000 genomes]
rs11054707	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054709	1.00[ASN][1000 genomes]
rs11054710	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054713	1.00[ASN][1000 genomes]
rs11054720	0.89[EUR][1000 genomes]
rs11054729	0.90[EUR][1000 genomes]
rs11054732	0.92[EUR][1000 genomes]
rs11054746	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054767	1.00[ASN][1000 genomes]
rs1123213	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829211	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831610	1.00[ASN][1000 genomes]
rs12296239	1.00[ASN][1000 genomes]
rs12297598	0.87[EUR][1000 genomes]
rs12305378	1.00[ASN][1000 genomes]
rs12306293	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12306537	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309246	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12309338	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12309495	0.80[AMR][1000 genomes]
rs12310020	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12311202	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316043	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12319942	0.90[EUR][1000 genomes]
rs12422890	1.00[ASN][1000 genomes]
rs12424332	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12424361	1.00[ASN][1000 genomes]
rs12425185	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425699	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12427198	0.83[EUR][1000 genomes]
rs13377971	1.00[ASN][1000 genomes]
rs16907789	1.00[ASN][1000 genomes]
rs28448423	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56259928	1.00[ASN][1000 genomes]
rs56998126	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57055264	0.89[EUR][1000 genomes]
rs59386755	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7308022	0.85[EUR][1000 genomes]
rs7311064	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061123	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74061145	0.87[EUR][1000 genomes]
rs7957531	0.89[EUR][1000 genomes]
rs7960716	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7973583	0.89[EUR][1000 genomes]
rs7973718	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7978064	0.90[EUR][1000 genomes]
rs7979919	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630249	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9630250	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9630266	0.80[AMR][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
rs58682800	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
4	chr12:12315400-12371600	Weak transcription	Lung	lung
5	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:12335200-12352000	Weak transcription	HSMM	muscle
11	chr12:12335200-12365800	Weak transcription	NHEK	skin
12	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
13	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:12336000-12354200	Weak transcription	Primary T cells from cord blood	blood
15	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
17	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
19	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
20	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:12338200-12355800	Weak transcription	Stomach Mucosa	stomach
22	chr12:12339200-12357600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:12340600-12359400	Weak transcription	Ovary	ovary
24	chr12:12342200-12360000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:12344000-12355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:12344000-12367800	Weak transcription	NHLF	lung
27	chr12:12344200-12351400	Weak transcription	Fetal Intestine Large	intestine
28	chr12:12344200-12352000	Weak transcription	Brain Anterior Caudate	brain
29	chr12:12344200-12353000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:12344200-12353200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:12344200-12353400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:12344200-12354000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:12344200-12355400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:12344200-12367200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:12344200-12367400	Weak transcription	Brain Substantia Nigra	brain
36	chr12:12344200-12367800	Weak transcription	NH-A	brain
37	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
38	chr12:12344400-12353000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:12344400-12353200	Weak transcription	Fetal Heart	heart
40	chr12:12344400-12354200	Weak transcription	K562	blood
41	chr12:12345600-12353000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:12346400-12353400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:12347200-12352000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:12347400-12355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:12347600-12367800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:12347800-12353000	Weak transcription	Osteobl	bone
47	chr12:12348400-12352400	ZNF genes & repeats	A549	lung
48	chr12:12348800-12367000	Weak transcription	HUVEC	blood vessel
49	chr12:12349000-12353400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:12349000-12367600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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