Variant report

Variant	rs12247017
Chromosome Location	chr10:97270729-97270730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12240292	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]
rs12244553	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];1.00[EUR][1000 genomes]
rs12772243	0.86[CEU][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12776555	0.86[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28419260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34597764	0.88[AFR][1000 genomes]
rs35793106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4918944	0.86[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4918947	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs749176	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3406864	chr10:97270544-97270918	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12247017	PIK3AP1	cis	parietal	SCAN
rs12247017	KIF11	cis	parietal	SCAN
rs12247017	IDE	cis	cerebellum	SCAN

Chromatin state (count:75 , 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	chr10:97260000-97272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:97260000-97278400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:97260800-97272800	Weak transcription	Esophagus	oesophagus
6	chr10:97261800-97271200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:97262000-97271800	Weak transcription	HMEC	breast
8	chr10:97262400-97271000	Weak transcription	Lung	lung
9	chr10:97262400-97275000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr10:97262400-97278400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:97265200-97271000	Weak transcription	Right Ventricle	heart
12	chr10:97265200-97272000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:97265400-97270800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:97266400-97271000	Weak transcription	Brain Angular Gyrus	brain
15	chr10:97266400-97272200	Weak transcription	Fetal Brain Male	brain
16	chr10:97266400-97272800	Weak transcription	Fetal Brain Female	brain
17	chr10:97266400-97273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:97267200-97271000	Weak transcription	Gastric	stomach
19	chr10:97267600-97275000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr10:97268600-97271000	Weak transcription	Brain Substantia Nigra	brain
21	chr10:97268800-97270800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:97268800-97272800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:97268800-97273000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:97269000-97270800	Weak transcription	Brain Hippocampus Middle	brain
25	chr10:97269000-97271000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:97269000-97271000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:97269000-97271000	Weak transcription	Placenta	Placenta
28	chr10:97269000-97271000	Weak transcription	Pancreas	Pancrea
29	chr10:97269000-97271000	Enhancers	Stomach Smooth Muscle	stomach
30	chr10:97269000-97271400	Weak transcription	Liver	Liver
31	chr10:97269000-97272200	Weak transcription	Psoas Muscle	Psoas
32	chr10:97269000-97272200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:97269000-97272400	Weak transcription	HSMMtube	muscle
34	chr10:97269000-97272800	Weak transcription	Small Intestine	intestine
35	chr10:97269000-97273000	Weak transcription	Ovary	ovary
36	chr10:97269000-97273000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr10:97269000-97277200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:97269000-97282600	Weak transcription	Fetal Kidney	kidney
39	chr10:97269200-97272400	Enhancers	Colon Smooth Muscle	Colon
40	chr10:97269200-97272800	Weak transcription	HUVEC	blood vessel
41	chr10:97269200-97273800	Weak transcription	Adipose Nuclei	Adipose
42	chr10:97269200-97277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:97269400-97271000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr10:97269400-97271400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr10:97269400-97272200	Weak transcription	Fetal Intestine Small	intestine
46	chr10:97269400-97272800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr10:97269400-97273000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:97269400-97273000	Weak transcription	Fetal Intestine Large	intestine
49	chr10:97269400-97273200	Weak transcription	NH-A	brain
50	chr10:97269400-97277200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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