Variant report

Variant	rs11638547
Chromosome Location	chr15:78463890-78463891
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78461657..78464169-chr15:78466113..78468967,2	MCF-7	breast:
2	chr15:78445643..78447208-chr15:78463043..78465753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103740	Chromatin interaction

Extended variants
information (count: 25 )
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];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[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];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[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];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634325	1.00[ASN][1000 genomes]
rs11638921	0.87[EUR][1000 genomes]
rs12904404	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904688	1.00[ASN][1000 genomes]
rs12904700	0.87[EUR][1000 genomes]
rs12906189	1.00[ASN][1000 genomes]
rs12910386	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]
rs12911405	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912695	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915634	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478430	1.00[JPT][hapmap]
rs1982241	0.86[EUR][1000 genomes]
rs2011323	1.00[JPT][hapmap]
rs2044098	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304825	0.89[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2868607	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087998	0.87[ASN][1000 genomes]
rs3816253	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs8035724	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11638547	IDH3A	cis	cerebellum	SCAN
rs11638547	IDH3A	cis	parietal	SCAN
rs11638547	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:78445800-78464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:78446600-78465200	Strong transcription	Fetal Intestine Large	intestine
4	chr15:78446800-78466000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:78447600-78464400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr15:78448000-78464200	Strong transcription	Liver	Liver
8	chr15:78448000-78465200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:78448000-78465800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:78448600-78465400	Strong transcription	Placenta	Placenta
11	chr15:78448800-78464200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:78448800-78466600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:78449000-78467800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:78449400-78465200	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr15:78449800-78465400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:78450000-78464600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:78450000-78465200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:78450000-78465200	Strong transcription	Osteobl	bone
19	chr15:78450000-78466200	Strong transcription	Left Ventricle	heart
20	chr15:78450200-78464200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:78450200-78465200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:78450200-78465400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:78450200-78465400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:78450600-78465200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:78451000-78464400	Strong transcription	Adipose Nuclei	Adipose
26	chr15:78451000-78466200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:78451200-78467000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr15:78451200-78467600	Strong transcription	Brain Cingulate Gyrus	brain
29	chr15:78451400-78464400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:78451400-78467200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:78452200-78467400	Strong transcription	Brain Angular Gyrus	brain
32	chr15:78452200-78467400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr15:78453400-78465200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:78453600-78464600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:78453600-78464600	Strong transcription	Colon Smooth Muscle	Colon
36	chr15:78453600-78467400	Strong transcription	Fetal Brain Female	brain
37	chr15:78454600-78467400	Strong transcription	Brain Substantia Nigra	brain
38	chr15:78454800-78465600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:78455600-78465000	Strong transcription	HSMM	muscle
40	chr15:78455800-78464800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:78455800-78465200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:78456000-78464800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:78456000-78465200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:78456400-78464200	Strong transcription	Fetal Stomach	stomach
45	chr15:78456600-78466200	Weak transcription	HUVEC	blood vessel
46	chr15:78457000-78464200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:78457000-78466800	Strong transcription	Rectal Smooth Muscle	rectum
48	chr15:78457000-78468400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:78458000-78465000	Strong transcription	Hela-S3	cervix
50	chr15:78458000-78465200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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