Variant report

Variant	rs892270
Chromosome Location	chr12:106478826-106478827
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF4	chr12:106478824-106479436	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
NUAK1	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10492351	0.82[JPT][hapmap]
rs10746054	0.85[CEU][hapmap]
rs12318540	0.82[JPT][hapmap]
rs1427793	0.82[JPT][hapmap]
rs1560761	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1896364	0.82[JPT][hapmap]
rs2436595	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][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
rs892270	CKAP4	cis	cerebellum	SCAN
rs892270	SLC41A2	cis	parietal	SCAN

Chromatin state (count:82 , 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	chr12:106462400-106482600	Weak transcription	Esophagus	oesophagus
4	chr12:106465200-106487000	Weak transcription	Brain Germinal Matrix	brain
5	chr12:106469000-106490200	Weak transcription	Gastric	stomach
6	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
7	chr12:106472400-106479400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:106472800-106480400	Weak transcription	Pancreas	Pancrea
9	chr12:106472800-106480600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:106473000-106482000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:106474600-106480000	Enhancers	NHDF-Ad	bronchial
12	chr12:106474600-106484600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:106474800-106479800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:106475000-106482400	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:106475400-106482200	Weak transcription	Psoas Muscle	Psoas
16	chr12:106475800-106484200	Weak transcription	Hela-S3	cervix
17	chr12:106476200-106479400	Enhancers	Fetal Heart	heart
18	chr12:106476400-106479400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:106476600-106483200	Weak transcription	Fetal Brain Male	brain
20	chr12:106477000-106480400	Enhancers	Brain Cingulate Gyrus	brain
21	chr12:106477000-106484400	Weak transcription	Lung	lung
22	chr12:106477000-106487200	Weak transcription	HepG2	liver
23	chr12:106477400-106479000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:106477400-106479200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:106477400-106479200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr12:106477600-106479000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:106477600-106479000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:106477600-106479200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:106477600-106492200	Weak transcription	Fetal Brain Female	brain
30	chr12:106477800-106479000	Enhancers	Fetal Stomach	stomach
31	chr12:106477800-106479200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr12:106477800-106479200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:106477800-106479400	Transcr. at gene 5' and 3'	A549	lung
34	chr12:106477800-106479400	Genic enhancers	HSMMtube	muscle
35	chr12:106477800-106479800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:106477800-106484400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:106478000-106479000	Enhancers	Fetal Lung	lung
38	chr12:106478000-106479800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:106478200-106479200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:106478200-106480200	Weak transcription	HUVEC	blood vessel
41	chr12:106478200-106480800	Weak transcription	Liver	Liver
42	chr12:106478200-106481600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:106478200-106482400	Weak transcription	Adipose Nuclei	Adipose
44	chr12:106478400-106479000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:106478400-106479200	Weak transcription	Right Ventricle	heart
46	chr12:106478400-106479400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:106478400-106479400	Enhancers	Osteobl	bone
48	chr12:106478400-106479600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:106478400-106479600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr12:106478400-106479800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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