Variant report

Variant	rs12240292
Chromosome Location	chr10:97273066-97273067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97255064..97257617-chr10:97271622..97273423,2	K562	blood:
2	chr10:97272650..97274953-chr10:97291349..97294026,2	K562	blood:
3	chr10:97271514..97273430-chr10:97278974..97280871,3	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12244553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12247017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12254671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12772243	0.86[CEU][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12776555	0.86[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28419260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34597764	0.88[AFR][1000 genomes]
rs35793106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4918944	0.86[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4918947	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs749176	1.00[AMR][1000 genomes];0.95[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	esv1808679	chr10:97266478-97316855	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12240292	PIK3AP1	cis	parietal	SCAN
rs12240292	KIF11	cis	parietal	SCAN
rs12240292	IDE	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97249800-97274000	Weak transcription	Spleen	Spleen
2	chr10:97256800-97273200	Weak transcription	HSMM	muscle
3	chr10:97260000-97278400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:97262400-97275000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:97262400-97278400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr10:97266400-97273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:97267600-97275000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr10:97269000-97277200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:97269000-97282600	Weak transcription	Fetal Kidney	kidney
10	chr10:97269200-97273800	Weak transcription	Adipose Nuclei	Adipose
11	chr10:97269200-97277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:97269400-97273200	Weak transcription	NH-A	brain
13	chr10:97269400-97277200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr10:97269600-97273400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr10:97269600-97277200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr10:97270200-97274600	Enhancers	HepG2	liver
17	chr10:97270600-97273800	Enhancers	Aorta	Aorta
18	chr10:97270600-97278200	Enhancers	Rectal Smooth Muscle	rectum
19	chr10:97270600-97278600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr10:97270600-97279200	Enhancers	Left Ventricle	heart
21	chr10:97270600-97279200	Enhancers	Right Atrium	heart
22	chr10:97270600-97279200	Enhancers	Stomach Mucosa	stomach
23	chr10:97270600-97283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr10:97270800-97275000	Enhancers	Brain Cingulate Gyrus	brain
25	chr10:97270800-97275000	Enhancers	Brain Hippocampus Middle	brain
26	chr10:97270800-97275600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:97270800-97275800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr10:97271000-97273600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr10:97271000-97273800	Enhancers	Pancreas	Pancrea
30	chr10:97271000-97274200	Enhancers	Lung	lung
31	chr10:97271000-97274600	Enhancers	Brain Substantia Nigra	brain
32	chr10:97271000-97275200	Enhancers	Brain Angular Gyrus	brain
33	chr10:97271000-97281200	Enhancers	Right Ventricle	heart
34	chr10:97271400-97275000	Enhancers	Liver	Liver
35	chr10:97271400-97275800	Weak transcription	Gastric	stomach
36	chr10:97271400-97279800	Enhancers	Fetal Muscle Leg	muscle
37	chr10:97271400-97279800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr10:97271600-97279800	Enhancers	Fetal Heart	heart
39	chr10:97271600-97284600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:97272000-97274400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:97272000-97275600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:97272000-97277400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr10:97272000-97277400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr10:97272200-97273600	Enhancers	Fetal Lung	lung
45	chr10:97272200-97274200	Enhancers	Fetal Intestine Small	intestine
46	chr10:97272200-97275000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr10:97272200-97275600	Enhancers	Fetal Brain Male	brain
48	chr10:97272200-97276000	Enhancers	Psoas Muscle	Psoas
49	chr10:97272400-97273200	Enhancers	K562	blood
50	chr10:97272400-97274800	Enhancers	HSMMtube	muscle

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