Variant report

Variant	rs8035724
Chromosome Location	chr15:78470542-78470543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:78469186-78470715	A549	lung:	n/a	chr15:78469893-78469909
2	CTCF	chr15:78469338-78470627	SK-N-SH	brain:	n/a	chr15:78469893-78469909

No.	Distal block	Cell Line	Cell type
1	chr15:78469629..78471471-chr15:78557003..78559345,2	MCF-7	breast:
2	chr15:78465044..78467906-chr15:78468275..78471070,3	K562	blood:
3	chr15:78439357..78441668-chr15:78468189..78471129,2	MCF-7	breast:
4	chr15:78465805..78468127-chr15:78469824..78472074,2	K562	blood:
5	chr15:78469404..78471342-chr15:78532874..78534838,21	MCF-7	breast:

Variant related genes	Relation type
ACSBG1	TF binding region
ENSG00000103740	Chromatin interaction
ENSG00000166411	Chromatin interaction
ENSG00000140403	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11072733	0.86[CHB][hapmap]
rs11072735	0.85[CHB][hapmap]
rs11629561	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11630776	0.88[CEU][hapmap]
rs11631100	0.84[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11631653	0.88[CEU][hapmap]
rs11638547	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11855354	0.82[MKK][hapmap]
rs12903696	0.83[MKK][hapmap]
rs12910386	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12911405	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12912695	0.88[EUR][1000 genomes]
rs12915634	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2044098	0.87[EUR][1000 genomes]
rs2304824	0.85[MKK][hapmap]
rs2304825	0.89[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2304826	0.86[CHB][hapmap]
rs2868607	0.86[EUR][1000 genomes]
rs3816253	0.89[CEU][hapmap]
rs7180781	0.86[CHB][hapmap]
rs8032618	0.82[MKK][hapmap]
rs9920103	0.83[ASW][hapmap];0.88[CHB][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap]
rs9972590	0.85[CHB][hapmap]
rs9972613	0.88[MKK][hapmap]

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
rs8035724	IDH3A	cis	cerebellum	SCAN
rs8035724	IDH3A	cis	Heart Left Ventricle	GTEx
rs8035724	IDH3A	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr15:78461800-78471000	Weak transcription	Psoas Muscle	Psoas
4	chr15:78464800-78475000	Weak transcription	HMEC	breast
5	chr15:78465200-78474200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:78465400-78475200	Weak transcription	NHEK	skin
10	chr15:78466800-78473200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:78466800-78473400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:78467000-78473200	Weak transcription	Aorta	Aorta
13	chr15:78467000-78473200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:78467000-78473400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:78467200-78477200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:78467400-78474800	Weak transcription	Fetal Brain Female	brain
17	chr15:78467400-78475400	Enhancers	Fetal Thymus	thymus
18	chr15:78467600-78472000	Weak transcription	Spleen	Spleen
19	chr15:78467800-78470800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:78468400-78471200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:78469600-78470600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr15:78469600-78470600	Enhancers	Right Ventricle	heart
23	chr15:78469600-78470600	Enhancers	HSMMtube	muscle
24	chr15:78469800-78470600	Enhancers	Brain Anterior Caudate	brain
25	chr15:78469800-78470600	Enhancers	Duodenum Mucosa	Duodenum
26	chr15:78469800-78471200	Enhancers	Fetal Muscle Leg	muscle
27	chr15:78469800-78471400	Enhancers	Fetal Muscle Trunk	muscle
28	chr15:78470000-78470600	Enhancers	HSMM	muscle
29	chr15:78470000-78472400	Genic enhancers	Thymus	Thymus
30	chr15:78470200-78471800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:78470200-78477000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:78470200-78486600	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:78470400-78493800	Weak transcription	Brain Substantia Nigra	brain

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