Variant report

Variant	rs1896364
Chromosome Location	chr12:106494345-106494346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106491668..106493233-chr12:106494081..106496361,2	MCF-7	breast:
2	chr12:106494133..106496771-chr12:106501271..106503780,3	MCF-7	breast:
3	chr12:106492655..106494743-chr12:106531247..106533400,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10492351	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10778458	0.95[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11112866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12318540	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17038091	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3782692	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964439	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55657928	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55748925	0.94[ASN][1000 genomes]
rs7138598	0.81[ASN][1000 genomes]
rs73193841	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73193855	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7485023	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892270	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1896364	CKAP4	cis	cerebellum	SCAN
rs1896364	NUAK1	cis	cerebellum	SCAN
rs1896364	CKAP4	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106458800-106500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:106461800-106499600	Weak transcription	Fetal Intestine Large	intestine
3	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
4	chr12:106485200-106500400	Weak transcription	HMEC	breast
5	chr12:106485400-106500800	Weak transcription	Lung	lung
6	chr12:106485600-106496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:106485600-106500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:106485800-106495000	Strong transcription	HSMMtube	muscle
9	chr12:106487400-106499400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:106487600-106500200	Weak transcription	NHLF	lung
11	chr12:106488600-106495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:106489600-106494600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:106490000-106496800	Weak transcription	Aorta	Aorta
14	chr12:106490600-106494600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:106490600-106498200	Weak transcription	Pancreas	Pancrea
16	chr12:106490800-106494800	Weak transcription	Fetal Stomach	stomach
17	chr12:106490800-106499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:106491000-106495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:106491000-106496600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:106491000-106499600	Weak transcription	Fetal Kidney	kidney
21	chr12:106491200-106494400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:106491200-106494600	Weak transcription	Gastric	stomach
23	chr12:106491200-106499800	Strong transcription	HSMM	muscle
24	chr12:106491200-106500000	Weak transcription	Fetal Lung	lung
25	chr12:106491200-106500800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:106491400-106495400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:106491400-106496600	Weak transcription	NHDF-Ad	bronchial
28	chr12:106491400-106499600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:106491600-106495200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:106491600-106495600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:106491600-106496000	Weak transcription	NH-A	brain
32	chr12:106491600-106497200	Strong transcription	Osteobl	bone
33	chr12:106491600-106497600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:106491800-106499600	Weak transcription	Ovary	ovary
35	chr12:106491800-106500400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:106492000-106498200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:106492000-106504400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:106492200-106495400	Weak transcription	HUVEC	blood vessel
39	chr12:106492400-106494400	Weak transcription	Fetal Brain Female	brain
40	chr12:106492600-106497400	Weak transcription	Psoas Muscle	Psoas
41	chr12:106492600-106499600	Weak transcription	Fetal Brain Male	brain
42	chr12:106492600-106500600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:106492600-106500800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr12:106492800-106494600	Weak transcription	Brain Angular Gyrus	brain
45	chr12:106492800-106500000	Weak transcription	NHEK	skin
46	chr12:106492800-106500600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:106493000-106494400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:106493000-106495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:106493200-106499600	Weak transcription	Brain Anterior Caudate	brain
50	chr12:106493200-106500000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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