Variant report

Variant	rs12882489
Chromosome Location	chr14:32926382-32926383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11156744	1.00[JPT][hapmap]
rs11156747	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11621072	0.85[CHB][hapmap]
rs11622937	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623071	1.00[ASN][1000 genomes]
rs12881167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12886529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12886735	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12891308	1.00[JPT][hapmap]
rs12894356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17410904	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951187	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs1957025	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1957026	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2383304	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34757755	1.00[ASN][1000 genomes]
rs34976846	1.00[ASN][1000 genomes]
rs61981143	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs941749	1.00[ASN][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	esv2758352	chr14:32858480-33016442	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759978	chr14:32858480-33016442	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12882489	SCFD1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32919200-32926400	Weak transcription	NHDF-Ad	bronchial
2	chr14:32919600-32926800	Weak transcription	Aorta	Aorta
3	chr14:32920800-32926600	Weak transcription	Brain Hippocampus Middle	brain
4	chr14:32920800-32930200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr14:32921600-32926400	Weak transcription	Brain Substantia Nigra	brain
6	chr14:32923800-32926400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr14:32923800-32926400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr14:32923800-32926400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr14:32923800-32926400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:32923800-32926400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr14:32923800-32926400	Weak transcription	Osteobl	bone
12	chr14:32923800-32927200	Weak transcription	HSMM	muscle
13	chr14:32923800-32927400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr14:32923800-32927800	Weak transcription	Colon Smooth Muscle	Colon
15	chr14:32923800-32929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:32923800-32929600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:32923800-32936400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:32924400-32928200	Enhancers	Rectal Smooth Muscle	rectum
19	chr14:32925000-32928200	Enhancers	Fetal Heart	heart
20	chr14:32926200-32926600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr14:32926200-32926800	Enhancers	Brain Cingulate Gyrus	brain
22	chr14:32926200-32927000	Enhancers	Brain Anterior Caudate	brain
23	chr14:32926200-32928200	Enhancers	Fetal Lung	lung
24	chr14:32926200-32928600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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