Variant report

Variant	rs12494055
Chromosome Location	chr3:42913845-42913846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13078406	0.83[JPT][hapmap]
rs13093968	0.90[GIH][hapmap];0.92[JPT][hapmap]
rs1896565	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288370	0.87[CHD][hapmap]
rs3732860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12494055	RTP3	cis	cerebellum	SCAN
rs12494055	HHATL	cis	parietal	SCAN
rs12494055	HHATL	cis	cerebellum	SCAN
rs12494055	XIRP1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42907000-42915800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:42909800-42914000	Weak transcription	HepG2	liver
3	chr3:42911400-42922000	Weak transcription	Gastric	stomach
4	chr3:42911800-42914800	Enhancers	Fetal Heart	heart
5	chr3:42912400-42921800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:42912600-42914000	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:42912600-42914400	Enhancers	Brain Germinal Matrix	brain
8	chr3:42912800-42914000	Flanking Active TSS	Liver	Liver
9	chr3:42912800-42914200	Enhancers	Right Ventricle	heart
10	chr3:42912800-42914200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:42912800-42914200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:42912800-42914400	Enhancers	Fetal Muscle Leg	muscle
13	chr3:42912800-42914400	Genic enhancers	Placenta	Placenta
14	chr3:42912800-42914400	Enhancers	Right Atrium	heart
15	chr3:42912800-42914600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:42913000-42914000	Enhancers	Fetal Kidney	kidney
17	chr3:42913000-42914000	Enhancers	HSMMtube	muscle
18	chr3:42913000-42914400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:42913000-42914400	Enhancers	Fetal Lung	lung
20	chr3:42913000-42914600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:42913000-42921400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:42913000-42922000	Weak transcription	Spleen	Spleen
23	chr3:42913200-42914000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:42913400-42914000	Enhancers	Brain Hippocampus Middle	brain
25	chr3:42913400-42914000	Enhancers	Pancreas	Pancrea
26	chr3:42913400-42914600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:42913600-42914400	Enhancers	Adipose Nuclei	Adipose
28	chr3:42913800-42914200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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