Variant report

Variant	rs2956406
Chromosome Location	chr12:106487563-106487564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106486379..106488971-chr12:106490561..106492780,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10746055	0.81[AMR][1000 genomes]
rs10861555	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11112867	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs11112868	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11112869	0.89[ASN][1000 genomes]
rs11112870	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112872	0.84[CHB][hapmap]
rs12371401	0.99[ASN][1000 genomes]
rs1427785	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1427786	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1560000	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2434082	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2436597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2436598	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2468198	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468199	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2468200	0.84[ASN][1000 genomes]
rs2569973	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7131912	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7964234	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs958422	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967872	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2956406	CKAP4	cis	parietal	SCAN
rs2956406	NUAK1	cis	cerebellum	SCAN

Chromatin state (count:79 , 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	chr12:106469000-106490200	Weak transcription	Gastric	stomach
4	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
5	chr12:106477600-106492200	Weak transcription	Fetal Brain Female	brain
6	chr12:106478400-106488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:106478400-106491600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:106478600-106492400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:106478800-106491000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:106479000-106489000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:106479000-106490600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:106479200-106490800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:106479200-106490800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:106479200-106491400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:106479400-106488400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:106479400-106490800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:106481000-106493000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr12:106482000-106489400	Enhancers	Brain Cingulate Gyrus	brain
19	chr12:106483000-106489800	Weak transcription	Liver	Liver
20	chr12:106483200-106488000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:106483200-106490400	Weak transcription	NHEK	skin
22	chr12:106483800-106491800	Weak transcription	Fetal Brain Male	brain
23	chr12:106484800-106491800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:106485200-106491600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:106485200-106500400	Weak transcription	HMEC	breast
26	chr12:106485400-106488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:106485400-106488600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:106485400-106489800	Weak transcription	Fetal Stomach	stomach
29	chr12:106485400-106490000	Weak transcription	Fetal Lung	lung
30	chr12:106485400-106490200	Weak transcription	Pancreas	Pancrea
31	chr12:106485400-106500800	Weak transcription	Lung	lung
32	chr12:106485600-106487600	Weak transcription	Aorta	Aorta
33	chr12:106485600-106487800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:106485600-106487800	Weak transcription	Right Atrium	heart
35	chr12:106485600-106488200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:106485600-106488600	Weak transcription	Right Ventricle	heart
37	chr12:106485600-106488600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:106485600-106489000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:106485600-106489400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:106485600-106489600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:106485600-106490400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:106485600-106490400	Weak transcription	NHDF-Ad	bronchial
43	chr12:106485600-106496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:106485600-106500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:106485800-106487800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:106485800-106489600	Weak transcription	Ovary	ovary
47	chr12:106485800-106495000	Strong transcription	HSMMtube	muscle
48	chr12:106486000-106489400	Enhancers	Brain Anterior Caudate	brain
49	chr12:106486000-106489800	Enhancers	Brain Angular Gyrus	brain
50	chr12:106486200-106487600	Weak transcription	Stomach Smooth Muscle	stomach

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