Variant report

Variant	rs12903696
Chromosome Location	chr15:78439018-78439019
allele	C/T
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	FOS	chr15:78438777-78439076	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr15:78438817-78439046	HepG2	liver:	n/a	chr15:78438902-78438913
3	CEBPB	chr15:78438688-78439372	HCT-116	colon:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
4	CEBPB	chr15:78438854-78439473	K562	blood:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
5	CEBPB	chr15:78438791-78439461	Hela-S3	cervix:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
6	CEBPB	chr15:78438795-78439220	A549	lung:	n/a	chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
7	CEBPB	chr15:78438830-78439504	HepG2	liver:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
8	BHLHE40	chr15:78438979-78439246	K562	blood:	n/a	n/a
9	MYC	chr15:78438891-78439022	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr15:78438726-78439366	A549	lung:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
11	CEBPB	chr15:78438746-78439330	ECC-1	luminal epithelium:	n/a	chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
12	CEBPB	chr15:78438840-78439257	ECC-1	luminal epithelium:	n/a	chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
13	FOS	chr15:78438751-78439866	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr15:78438711-78439440	MCF-7	breast:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
15	CEBPB	chr15:78438804-78439498	A549	lung:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
16	STAT3	chr15:78438787-78439775	MCF10A-Er-Src	breast:	n/a	chr15:78439015-78439023
17	CEBPB	chr15:78438733-78439449	MCF-7	breast:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
18	CEBPB	chr15:78438825-78439220	H1-hESC	embryonic stem cell:	n/a	chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
19	FOS	chr15:78438776-78439905	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr15:78438900-78439121	K562	blood:	n/a	chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
21	CEBPB	chr15:78438826-78439494	IMR90	lung:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023
22	CEBPB	chr15:78438831-78439531	K562	blood:	n/a	chr15:78439329-78439340 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439014-78439023 chr15:78439013-78439024 chr15:78439012-78439025 chr15:78439012-78439025 chr15:78439014-78439023

No.	Distal block	Cell Line	Cell type
1	chr15:78438626..78440576-chr15:78459614..78461953,2	K562	blood:
2	chr15:78414752..78417603-chr15:78438939..78440752,2	MCF-7	breast:
3	chr15:78421103..78425437-chr15:78438436..78443517,9	MCF-7	breast:
4	chr15:78437153..78440009-chr15:78444178..78446804,3	MCF-7	breast:
5	chr15:78437349..78439944-chr15:78555293..78556889,2	MCF-7	breast:
6	chr15:78422180..78427678-chr15:78438636..78444300,13	MCF-7	breast:
7	chr15:78422233..78425731-chr15:78438987..78443227,7	K562	blood:
8	chr15:78437651..78440580-chr15:78459542..78461046,2	MCF-7	breast:
9	chr15:78437413..78439918-chr15:78471623..78473708,2	K562	blood:

Variant related genes	Relation type
IDH3A	TF binding region
ENSG00000103740	Chromatin interaction
ENSG00000166411	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000140403	Chromatin interaction
ENSG00000259708	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]
rs11855354	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];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982242	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304824	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]
rs3816253	0.80[MEX][hapmap]
rs6495275	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495276	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7172176	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8032618	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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034946	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8035724	0.83[MKK][hapmap]
rs9920103	0.89[CEU][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs9972613	0.80[ASW][hapmap];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];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[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
rs12903696	IDH3A	cis	Heart Left Ventricle	GTEx
rs12903696	IDH3A	cis	cerebellum	SCAN
rs12903696	IDH3A	cis	parietal	SCAN

Chromatin state (count:44 , 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	chr15:78427200-78439200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:78432600-78440200	Weak transcription	Small Intestine	intestine
6	chr15:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:78433600-78440400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:78433800-78440200	Weak transcription	Right Ventricle	heart
9	chr15:78434000-78439800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:78434800-78439200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:78435200-78440400	Weak transcription	HepG2	liver
12	chr15:78436000-78440600	Weak transcription	Thymus	Thymus
13	chr15:78437000-78440000	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:78437600-78440600	Weak transcription	HSMM	muscle
15	chr15:78438200-78441000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:78438400-78439200	Enhancers	Fetal Intestine Small	intestine
17	chr15:78438400-78440400	Weak transcription	Liver	Liver
18	chr15:78438400-78440800	Enhancers	Adipose Nuclei	Adipose
19	chr15:78438400-78440800	Enhancers	Fetal Intestine Large	intestine
20	chr15:78438400-78441000	Enhancers	Psoas Muscle	Psoas
21	chr15:78438600-78439800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:78438600-78440600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:78438600-78440600	Enhancers	Hela-S3	cervix
24	chr15:78438600-78440600	Enhancers	NHEK	skin
25	chr15:78438600-78440800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr15:78438600-78441000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr15:78438600-78441000	Enhancers	Placenta	Placenta
28	chr15:78438800-78439400	Enhancers	Left Ventricle	heart
29	chr15:78438800-78439800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:78438800-78440400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:78438800-78440600	Enhancers	K562	blood
32	chr15:78438800-78440800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:78438800-78440800	Enhancers	HMEC	breast
34	chr15:78438800-78441000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:78438800-78441200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:78439000-78439200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr15:78439000-78439200	Enhancers	Fetal Thymus	thymus
38	chr15:78439000-78440000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:78439000-78440000	Weak transcription	Right Atrium	heart
40	chr15:78439000-78440400	Enhancers	A549	lung
41	chr15:78439000-78440600	Weak transcription	NHDF-Ad	bronchial
42	chr15:78439000-78440800	Enhancers	Esophagus	oesophagus
43	chr15:78439000-78440800	Enhancers	Fetal Heart	heart
44	chr15:78439000-78440800	Enhancers	Pancreas	Pancrea

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