Variant report

Variant	rs6495275
Chromosome Location	chr15:78436817-78436818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
IDH3A	TF binding region
ENSG00000166411	Chromatin interaction
ENSG00000103740	Chromatin interaction
ENSG00000136425	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11855354	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903696	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915990	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1982242	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304824	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495276	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7172176	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8032618	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034946	0.90[ASN][1000 genomes]
rs9920103	0.85[EUR][1000 genomes]
rs9972613	0.81[AFR][1000 genomes];0.89[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6495275	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78424600-78440800	Weak transcription	HSMMtube	muscle
2	chr15:78425000-78440600	Weak transcription	Fetal Stomach	stomach
3	chr15:78426000-78440200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:78427200-78438600	Weak transcription	Placenta	Placenta
5	chr15:78427200-78439200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:78432600-78440200	Weak transcription	Small Intestine	intestine
7	chr15:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:78433600-78440400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:78433800-78440200	Weak transcription	Right Ventricle	heart
10	chr15:78434000-78439800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:78434800-78439200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:78435200-78438600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:78435200-78438800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:78435200-78438800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:78435200-78440400	Weak transcription	HepG2	liver
16	chr15:78435400-78438400	Weak transcription	Fetal Intestine Large	intestine
17	chr15:78435400-78438400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:78436000-78440600	Weak transcription	Thymus	Thymus
19	chr15:78436800-78437600	Enhancers	Adipose Nuclei	Adipose

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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