Variant report

Variant	rs56087862
Chromosome Location	chr12:12397654-12397655
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12395975..12398553-chr12:12399397..12402094,2	MCF-7	breast:
2	chr12:12393044..12397840-chr12:12419223..12421821,5	MCF-7	breast:
3	chr12:12390182..12397827-chr12:12417123..12421502,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction
ENSG00000270857	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10466849	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834671	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297598	0.80[AMR][1000 genomes]
rs12299540	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317629	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321417	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425946	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427198	0.80[AMR][1000 genomes]
rs74061128	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.80[AMR][1000 genomes]
rs74061156	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061161	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs56087862	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 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	chr12:12377800-12407200	Weak transcription	NH-A	brain
3	chr12:12384800-12417200	Weak transcription	K562	blood
4	chr12:12385000-12404000	Weak transcription	Lung	lung
5	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
7	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
8	chr12:12390400-12398800	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:12390400-12400400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:12391200-12399600	Weak transcription	HSMM	muscle
12	chr12:12392200-12403000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:12392400-12407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:12392600-12408200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:12392800-12399800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:12393200-12405000	Weak transcription	HUVEC	blood vessel
17	chr12:12393400-12399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:12393800-12399000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:12394200-12400600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:12394200-12407200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:12394200-12407200	Weak transcription	Osteobl	bone
22	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
24	chr12:12394400-12401000	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:12394600-12407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:12394800-12405800	Weak transcription	HMEC	breast
27	chr12:12394800-12407600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:12395000-12397800	Active TSS	Brain Anterior Caudate	brain
30	chr12:12395200-12397800	Active TSS	Brain Hippocampus Middle	brain
31	chr12:12395200-12407200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:12395400-12397800	Active TSS	Brain Substantia Nigra	brain
33	chr12:12395600-12398200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:12395600-12399400	Weak transcription	Fetal Brain Female	brain
35	chr12:12395600-12409200	Weak transcription	Ovary	ovary
36	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:12395800-12398400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:12395800-12406600	Weak transcription	Brain Germinal Matrix	brain
39	chr12:12396000-12398200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:12396000-12407400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:12396400-12398000	Active TSS	Brain Cingulate Gyrus	brain
42	chr12:12396600-12397800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:12396600-12397800	Weak transcription	HepG2	liver
44	chr12:12397000-12399200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:12397000-12403600	Weak transcription	Fetal Intestine Small	intestine
46	chr12:12397000-12408400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:12397200-12399200	Weak transcription	HSMMtube	muscle
48	chr12:12397200-12399800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:12397400-12398000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:12397400-12399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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