Variant report

Variant	rs12910386
Chromosome Location	chr15:78472644-78472645
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11629561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630776	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11631100	0.84[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631653	0.88[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11634325	1.00[ASN][1000 genomes]
rs11638547	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638921	0.87[EUR][1000 genomes]
rs12904404	1.00[ASN][1000 genomes]
rs12904688	1.00[ASN][1000 genomes]
rs12904700	0.87[EUR][1000 genomes]
rs12906189	1.00[ASN][1000 genomes]
rs12911405	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912695	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478430	1.00[JPT][hapmap]
rs1982241	0.85[EUR][1000 genomes]
rs2011323	1.00[JPT][hapmap]
rs2044098	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304825	0.89[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2868607	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087998	0.87[ASN][1000 genomes]
rs3816253	0.89[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs8035724	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12910386	IDH3A	cis	Heart Left Ventricle	GTEx
rs12910386	IDH3A	cis	cerebellum	SCAN
rs12910386	IDH3A	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78460200-78474200	Weak transcription	HepG2	liver
3	chr15:78464800-78475000	Weak transcription	HMEC	breast
4	chr15:78465200-78474200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:78465400-78475200	Weak transcription	NHEK	skin
9	chr15:78466800-78473200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:78466800-78473400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:78467000-78473200	Weak transcription	Aorta	Aorta
12	chr15:78467000-78473200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:78467000-78473400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:78467200-78477200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:78467400-78474800	Weak transcription	Fetal Brain Female	brain
16	chr15:78467400-78475400	Enhancers	Fetal Thymus	thymus
17	chr15:78470200-78477000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:78470200-78486600	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:78470400-78493800	Weak transcription	Brain Substantia Nigra	brain
20	chr15:78470600-78477200	Weak transcription	Brain Anterior Caudate	brain
21	chr15:78470600-78486600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:78471200-78475800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:78471400-78472800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:78472000-78473600	Enhancers	Spleen	Spleen
25	chr15:78472400-78473800	Enhancers	Thymus	Thymus
26	chr15:78472400-78475400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:78472600-78473400	Enhancers	Fetal Muscle Leg	muscle

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