Variant report

Variant	rs2304824
Chromosome Location	chr15:78466127-78466128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78455141..78458694-chr15:78463989..78467554,5	MCF-7	breast:
2	chr15:78425346..78429501-chr15:78464309..78466788,4	MCF-7	breast:
3	chr15:78421965..78424193-chr15:78465887..78467751,2	K562	blood:
4	chr15:78441557..78443629-chr15:78465322..78467706,2	MCF-7	breast:
5	chr15:78447133..78448969-chr15:78464297..78466316,2	K562	blood:

Variant related genes	Relation type
ENSG00000136425	Chromatin interaction
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11072738	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11855354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12903696	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1982242	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495275	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495276	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7172176	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8034946	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035724	0.85[MKK][hapmap]
rs9920103	0.85[CEU][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.85[EUR][1000 genomes]
rs9972613	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][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
rs2304824	IDH3A	cis	Heart Left Ventricle	GTEx
rs2304824	IDH3A	cis	parietal	SCAN
rs2304824	IDH3A	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78448800-78466600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:78449000-78467800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:78450000-78466200	Strong transcription	Left Ventricle	heart
5	chr15:78451000-78466200	Strong transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:78451200-78467000	Strong transcription	Stomach Smooth Muscle	stomach
7	chr15:78451200-78467600	Strong transcription	Brain Cingulate Gyrus	brain
8	chr15:78451400-78467200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:78452200-78467400	Strong transcription	Brain Angular Gyrus	brain
10	chr15:78452200-78467400	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr15:78453600-78467400	Strong transcription	Fetal Brain Female	brain
12	chr15:78454600-78467400	Strong transcription	Brain Substantia Nigra	brain
13	chr15:78456600-78466200	Weak transcription	HUVEC	blood vessel
14	chr15:78457000-78466800	Strong transcription	Rectal Smooth Muscle	rectum
15	chr15:78457000-78468400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:78458200-78466600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:78458800-78468800	Weak transcription	Stomach Mucosa	stomach
18	chr15:78459000-78470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:78460200-78466400	Weak transcription	Fetal Brain Male	brain
20	chr15:78460200-78474200	Weak transcription	HepG2	liver
21	chr15:78460400-78467000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:78461000-78466600	Strong transcription	Pancreas	Pancrea
23	chr15:78461800-78467000	Strong transcription	Aorta	Aorta
24	chr15:78461800-78471000	Weak transcription	Psoas Muscle	Psoas
25	chr15:78462000-78467200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:78462000-78468000	Strong transcription	Gastric	stomach
27	chr15:78463000-78468200	Enhancers	Primary B cells from peripheral blood	blood
28	chr15:78463400-78466400	Strong transcription	A549	lung
29	chr15:78463400-78466800	Strong transcription	Brain Anterior Caudate	brain
30	chr15:78463400-78467600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr15:78463800-78466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:78464200-78466200	Weak transcription	NHLF	lung
33	chr15:78464200-78466800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:78464200-78467000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:78464200-78467200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:78464600-78466200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:78464600-78466200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:78464600-78466200	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:78464600-78466400	Weak transcription	Small Intestine	intestine
40	chr15:78464600-78466800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:78464600-78467200	Strong transcription	Fetal Stomach	stomach
42	chr15:78464600-78467400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:78464600-78468000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:78464600-78469800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:78464800-78466400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:78464800-78466400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:78464800-78466400	Strong transcription	Adipose Nuclei	Adipose
48	chr15:78464800-78466400	Weak transcription	Ovary	ovary
49	chr15:78464800-78466600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:78464800-78466800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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