Variant report

Variant	rs11855354
Chromosome Location	chr15:78443631-78443632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78441624..78443874-chr15:78458194..78460448,2	K562	blood:
2	chr15:78442888..78445461-chr15:78457848..78460341,2	MCF-7	breast:
3	chr15:78439170..78443635-chr15:78452310..78455814,4	K562	blood:
4	chr15:78440356..78444633-chr15:78445807..78449726,8	K562	blood:
5	chr15:78440859..78443747-chr15:78450376..78455479,5	K562	blood:
6	chr15:78422180..78427678-chr15:78438636..78444300,13	MCF-7	breast:

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:14)

rs_ID	r²[population]
rs11072738	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs12903696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982242	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304824	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]
rs3816253	0.80[MEX][hapmap]
rs6495275	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495276	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7172176	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8032618	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034946	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8035724	0.82[MKK][hapmap]
rs9920103	0.89[CEU][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9972613	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11855354	IDH3A	cis	Heart Left Ventricle	GTEx
rs11855354	IDH3A	cis	parietal	SCAN
rs11855354	IDH3A	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78442400-78443800	Flanking Active TSS	Dnd41	blood
2	chr15:78442600-78443800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:78442600-78443800	Enhancers	Gastric	stomach
4	chr15:78442600-78444200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr15:78442600-78445200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:78442600-78447400	Weak transcription	Aorta	Aorta
7	chr15:78442600-78448000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:78442600-78451200	Weak transcription	Lung	lung
9	chr15:78442600-78451400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:78442600-78458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:78442800-78443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:78442800-78444000	Enhancers	Psoas Muscle	Psoas
13	chr15:78442800-78444400	Enhancers	Small Intestine	intestine
14	chr15:78442800-78445400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:78442800-78445400	Weak transcription	HSMM	muscle
16	chr15:78442800-78445400	Weak transcription	HSMMtube	muscle
17	chr15:78442800-78447200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:78442800-78448000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:78442800-78448000	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:78442800-78448600	Weak transcription	Placenta	Placenta
21	chr15:78442800-78448800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:78442800-78449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:78442800-78450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:78442800-78450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:78442800-78451800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:78442800-78451800	Weak transcription	Ovary	ovary
27	chr15:78442800-78452200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:78442800-78463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:78443000-78444200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:78443000-78445400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:78443000-78445400	Weak transcription	Fetal Intestine Large	intestine
33	chr15:78443000-78445400	Weak transcription	Osteobl	bone
34	chr15:78443000-78446800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:78443000-78450000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:78443000-78450000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:78443000-78450200	Weak transcription	Fetal Stomach	stomach
38	chr15:78443000-78451600	Weak transcription	NH-A	brain
39	chr15:78443000-78452200	Weak transcription	HUVEC	blood vessel
40	chr15:78443200-78443800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr15:78443200-78444200	Flanking Active TSS	GM12878-XiMat	blood
42	chr15:78443200-78444400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:78443200-78445600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:78443200-78447000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:78443200-78447200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:78443200-78447200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:78443200-78451200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:78443200-78451400	Weak transcription	Fetal Brain Female	brain
49	chr15:78443200-78451600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:78443200-78451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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