Variant report

Variant	rs754724
Chromosome Location	chr12:106503474-106503475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106494133..106496771-chr12:106501271..106503780,3	MCF-7	breast:
2	chr12:106501658..106504096-chr12:106533862..106535852,2	MCF-7	breast:
3	chr12:106499591..106503536-chr12:106504416..106508585,6	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10746055	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861555	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112867	0.94[CHB][hapmap]
rs11112868	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112870	0.83[EUR][1000 genomes]
rs11112872	0.84[CHB][hapmap]
rs1427785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1427786	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1560000	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs2436597	1.00[CHB][hapmap]
rs2468199	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2569973	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3782695	0.84[EUR][1000 genomes]
rs7131912	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7132167	0.81[CEU][hapmap]
rs7964234	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs967872	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs754724	CKAP4	cis	parietal	SCAN
rs754724	WSCD2	cis	parietal	SCAN
rs754724	NUAK1	cis	cerebellum	SCAN
rs754724	ASCL4	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106492000-106504400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:106493400-106512400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:106495600-106507200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr12:106498400-106507200	Weak transcription	Pancreas	Pancrea
5	chr12:106499400-106503800	Enhancers	Brain Germinal Matrix	brain
6	chr12:106499400-106504000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:106499400-106505400	Enhancers	Fetal Intestine Small	intestine
8	chr12:106499600-106503600	Enhancers	Brain Anterior Caudate	brain
9	chr12:106499600-106503600	Enhancers	Hela-S3	cervix
10	chr12:106499600-106503800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr12:106499600-106504200	Enhancers	Fetal Brain Male	brain
12	chr12:106499600-106504600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:106499600-106505000	Enhancers	Fetal Intestine Large	intestine
14	chr12:106499600-106505000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:106499600-106505200	Enhancers	Brain Cingulate Gyrus	brain
16	chr12:106499600-106511400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:106499800-106507800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:106499800-106508400	Genic enhancers	HSMM	muscle
19	chr12:106500000-106503800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:106500000-106503800	Enhancers	Fetal Lung	lung
21	chr12:106500000-106506200	Enhancers	NHEK	skin
22	chr12:106500000-106507000	Enhancers	Adipose Nuclei	Adipose
23	chr12:106500000-106507400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:106500000-106510000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr12:106500200-106503600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:106500200-106503600	Enhancers	Aorta	Aorta
27	chr12:106500200-106505200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:106500200-106507400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:106500200-106510200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:106500200-106514000	Enhancers	Liver	Liver
31	chr12:106500400-106505400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:106500400-106505800	Enhancers	Brain Substantia Nigra	brain
33	chr12:106500600-106504400	Enhancers	Left Ventricle	heart
34	chr12:106500600-106504600	Enhancers	H9 Cell Line	embryonic stem cell
35	chr12:106500600-106507400	Enhancers	HepG2	liver
36	chr12:106500600-106508600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:106500600-106508600	Enhancers	Right Atrium	heart
38	chr12:106500800-106504600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:106500800-106504600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:106500800-106506200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:106500800-106507600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:106500800-106510200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:106500800-106521800	Enhancers	Brain Angular Gyrus	brain
44	chr12:106501000-106504200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:106501000-106505000	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr12:106501200-106504200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:106501200-106504200	Enhancers	Colonic Mucosa	Colon
48	chr12:106501200-106516800	Enhancers	Right Ventricle	heart
49	chr12:106501400-106510400	Enhancers	Fetal Brain Female	brain
50	chr12:106501600-106503600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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