Variant report

Variant	rs12317629
Chromosome Location	chr12:12404903-12404904
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	chr12:12400936..12406172-chr12:12417674..12422348,4	K562	blood:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10466849	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845499	0.81[AMR][1000 genomes]
rs11834671	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299540	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321417	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087862	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061128	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061161	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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
rs12317629	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 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	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
6	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
7	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:12392400-12407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:12392600-12408200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:12393200-12405000	Weak transcription	HUVEC	blood vessel
11	chr12:12394200-12407200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:12394200-12407200	Weak transcription	Osteobl	bone
13	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
15	chr12:12394600-12407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:12394800-12405800	Weak transcription	HMEC	breast
17	chr12:12394800-12407600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:12395200-12407200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:12395600-12409200	Weak transcription	Ovary	ovary
21	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:12395800-12406600	Weak transcription	Brain Germinal Matrix	brain
23	chr12:12396000-12407400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:12397000-12408400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:12397400-12409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:12397600-12406200	Weak transcription	Primary T cells from cord blood	blood
27	chr12:12397600-12407600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:12397600-12409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:12397600-12416600	Weak transcription	Fetal Stomach	stomach
30	chr12:12397800-12405200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:12397800-12416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:12397800-12417200	Weak transcription	Brain Anterior Caudate	brain
33	chr12:12398200-12407400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:12398400-12406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:12401000-12407200	Weak transcription	Liver	Liver
36	chr12:12401000-12408200	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:12401200-12406800	Weak transcription	HepG2	liver
38	chr12:12401200-12408200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:12401200-12409200	Weak transcription	Right Atrium	heart
40	chr12:12401200-12418000	Weak transcription	Brain Substantia Nigra	brain
41	chr12:12402000-12407400	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:12402400-12417200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:12402800-12408000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:12403000-12408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:12403400-12407600	Weak transcription	A549	lung
46	chr12:12403600-12406200	Strong transcription	Fetal Intestine Small	intestine
47	chr12:12403600-12408200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:12404400-12405000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:12404600-12405200	Enhancers	Lung	lung
50	chr12:12404600-12405800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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