Variant report

Variant	rs56998126
Chromosome Location	chr12:12367992-12367993
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: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10082834	0.85[EUR][1000 genomes]
rs10083170	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	0.84[AFR][1000 genomes]
rs10845497	0.96[EUR][1000 genomes]
rs10845499	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.87[EUR][1000 genomes]
rs11054720	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	0.92[EUR][1000 genomes]
rs11829211	0.83[EUR][1000 genomes]
rs12297598	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12311922	0.96[EUR][1000 genomes]
rs12319942	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12427198	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448423	0.96[EUR][1000 genomes]
rs57055264	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308022	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74061123	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.84[AMR][1000 genomes];0.94[EUR][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
rs56998126	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12315400-12371600	Weak transcription	Lung	lung
2	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
3	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
4	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
5	chr12:12354800-12370400	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:12355400-12369400	Weak transcription	Adipose Nuclei	Adipose
7	chr12:12355600-12369800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:12355800-12374200	Weak transcription	Fetal Intestine Large	intestine
9	chr12:12356000-12368800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:12356000-12369000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:12356000-12370000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:12360400-12368000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:12360800-12369000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:12360800-12374600	Weak transcription	Ovary	ovary
15	chr12:12361000-12369200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:12362200-12370000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:12364600-12370000	Weak transcription	GM12878-XiMat	blood
18	chr12:12366000-12369000	Weak transcription	Liver	Liver
19	chr12:12366400-12369200	Flanking Active TSS	A549	lung
20	chr12:12366600-12368200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr12:12366800-12368000	Weak transcription	HSMM	muscle
22	chr12:12367000-12368000	Enhancers	Brain Hippocampus Middle	brain
23	chr12:12367000-12368600	Enhancers	HUVEC	blood vessel
24	chr12:12367200-12368000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr12:12367200-12368000	Enhancers	Colon Smooth Muscle	Colon
26	chr12:12367200-12368000	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr12:12367200-12368200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:12367400-12368000	Enhancers	Fetal Lung	lung
29	chr12:12367400-12368200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:12367400-12368200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr12:12367400-12368200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr12:12367400-12368200	Enhancers	Brain Substantia Nigra	brain
33	chr12:12367400-12368200	Enhancers	Stomach Mucosa	stomach
34	chr12:12367600-12368000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:12367600-12368000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr12:12367600-12368000	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:12367600-12368000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr12:12367600-12368200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:12367600-12368200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr12:12367600-12368200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:12367600-12368200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr12:12367600-12368200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr12:12367600-12368200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:12367600-12368200	Enhancers	Brain Angular Gyrus	brain
45	chr12:12367600-12368200	Enhancers	Duodenum Mucosa	Duodenum
46	chr12:12367600-12368200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:12367600-12368200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:12367600-12368200	Enhancers	Osteobl	bone
49	chr12:12367600-12368400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:12367600-12368600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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