Variant report

Variant	rs12440067
Chromosome Location	chr15:41782728-41782729
allele	A/C
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	JUND	chr15:41782364-41783074	SK-N-SH	brain:	n/a	chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693 chr15:41782682-41782693
2	ELK1	chr15:41782686-41782894	Hela-S3	cervix:	n/a	n/a
3	IRF4	chr15:41782450-41782971	GM12878	blood:	n/a	n/a
4	YY1	chr15:41782655-41782897	GM12878	blood:	n/a	n/a
5	RAD21	chr15:41782535-41782892	IMR90	lung:	n/a	n/a
6	MAZ	chr15:41782614-41782856	GM12878	blood:	n/a	chr15:41782683-41782692
7	ATF1	chr15:41782576-41782908	K562	blood:	n/a	n/a
8	MEF2A	chr15:41782509-41782853	GM12878	blood:	n/a	n/a
9	FOSL2	chr15:41782430-41783078	SK-N-SH	brain:	n/a	chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693
10	MTA3	chr15:41782446-41783071	GM12878	blood:	n/a	n/a
11	EP300	chr15:41782531-41782923	Hela-S3	cervix:	n/a	chr15:41782684-41782693 chr15:41782683-41782692
12	BATF	chr15:41782591-41782927	GM12878	blood:	n/a	chr15:41782680-41782691
13	FOS	chr15:41782504-41782939	MCF10A-Er-Src	breast:	n/a	chr15:41782732-41782743 chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693 chr15:41782682-41782693
14	PML	chr15:41782366-41782983	GM12878	blood:	n/a	chr15:41782685-41782694
15	BRCA1	chr15:41782603-41782830	Hela-S3	cervix:	n/a	n/a
16	FOSL2	chr15:41782441-41782948	SK-N-SH	brain:	n/a	chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693
17	MAFK	chr15:41782622-41782848	Hela-S3	cervix:	n/a	n/a
18	JUN	chr15:41782508-41782923	HUVEC	blood vessel:	n/a	chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693
19	MAZ	chr15:41782641-41782873	Hela-S3	cervix:	n/a	chr15:41782683-41782692
20	FOSL1	chr15:41782399-41783106	HCT-116	colon:	n/a	chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693
21	CEBPB	chr15:41782603-41782839	A549	lung:	n/a	n/a
22	YY1	chr15:41782459-41782758	GM12891	blood:	n/a	n/a
23	FOS	chr15:41782503-41782966	MCF10A-Er-Src	breast:	n/a	chr15:41782732-41782743 chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693 chr15:41782682-41782693
24	TBL1XR1	chr15:41782708-41782785	K562	blood:	n/a	n/a
25	JUND	chr15:41782443-41783114	SK-N-SH	brain:	n/a	chr15:41782684-41782692 chr15:41782685-41782692 chr15:41782684-41782693 chr15:41782682-41782693
26	BCLAF1	chr15:41782531-41782962	GM12878	blood:	n/a	chr15:41782683-41782692 chr15:41782684-41782693
27	POLR2A	chr15:41782588-41782932	HUVEC	blood vessel:	n/a	n/a
28	EP300	chr15:41782594-41782863	GM12878	blood:	n/a	chr15:41782684-41782693 chr15:41782683-41782692
29	MEF2A	chr15:41782597-41782864	K562	blood:	n/a	n/a
30	NFIC	chr15:41782403-41782981	GM12878	blood:	n/a	n/a
31	YY1	chr15:41782415-41782939	SK-N-SH	brain:	n/a	n/a
32	CEBPB	chr15:41782358-41783011	GM12878	blood:	n/a	n/a
33	ZNF384	chr15:41782486-41782784	GM12878	blood:	n/a	chr15:41782638-41782646
34	MAX	chr15:41782478-41782949	SK-N-SH	brain:	n/a	chr15:41782683-41782692
35	ARID3A	chr15:41782643-41782757	K562	blood:	n/a	n/a
36	STAT3	chr15:41782538-41782903	MCF10A-Er-Src	breast:	n/a	chr15:41782684-41782693 chr15:41782683-41782692
37	CUX1	chr15:41782690-41782738	K562	blood:	n/a	n/a
38	MYC	chr15:41782577-41782895	MCF10A-Er-Src	breast:	n/a	chr15:41782683-41782692
39	FOXM1	chr15:41782477-41782993	GM12878	blood:	n/a	n/a
40	BATF	chr15:41782490-41782964	GM12878	blood:	n/a	chr15:41782680-41782691
41	SP1	chr15:41782545-41782939	GM12878	blood:	n/a	n/a
42	TCF12	chr15:41782315-41783083	SK-N-SH	brain:	n/a	chr15:41782725-41782733
43	PBX3	chr15:41782415-41783000	SK-N-SH	brain:	n/a	n/a
44	NFATC1	chr15:41782430-41782963	GM12878	blood:	n/a	n/a
45	RFX5	chr15:41782576-41782876	Hela-S3	cervix:	n/a	n/a
46	SRF	chr15:41782633-41782820	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:41782481-41782962	HCT-116	colon:	n/a	n/a
48	USF2	chr15:41782615-41782882	Hela-S3	cervix:	n/a	n/a
49	TCF7L2	chr15:41782526-41782888	Hela-S3	cervix:	n/a	n/a
50	SMC3	chr15:41782535-41782926	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41773035..41782898-chr15:41783132..41789747,15	K562	blood:
2	chr15:41767730..41772843-chr15:41782564..41789351,11	K562	blood:
3	chr15:41524238..41526423-chr15:41781115..41782836,2	K562	blood:

Variant related genes	Relation type
ITPKA	TF binding region
ENSG00000137815	Chromatin interaction
ENSG00000137825	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12440111	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12440067	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs12440067	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs12440067	OIP5-AS1	cis	Artery Tibial	GTEx
rs12440067	NDUFAF1	cis	Esophagus Mucosa	GTEx
rs12440067	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs12440067	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs12440067	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs12440067	NDUFAF1	cis	multi-tissue	Pritchard
rs12440067	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs12440067	NDUFAF1	cis	Muscle Skeletal	GTEx
rs12440067	OIP5-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41773400-41785000	Weak transcription	A549	lung
2	chr15:41773800-41784000	Weak transcription	HepG2	liver
3	chr15:41774800-41784600	Weak transcription	Dnd41	blood
4	chr15:41775400-41784800	Weak transcription	Liver	Liver
5	chr15:41775600-41783800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:41775600-41784800	Weak transcription	Brain Angular Gyrus	brain
7	chr15:41776000-41782800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:41776000-41784400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:41776000-41784800	Weak transcription	Brain Germinal Matrix	brain
10	chr15:41776200-41782800	Weak transcription	Primary B cells from cord blood	blood
11	chr15:41776400-41783600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:41776400-41783800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:41776800-41784200	Weak transcription	K562	blood
14	chr15:41776800-41784600	Weak transcription	Placenta	Placenta
15	chr15:41777200-41783000	Weak transcription	Fetal Brain Female	brain
16	chr15:41778600-41784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:41779000-41783800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:41779800-41785200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:41780200-41783600	Weak transcription	Fetal Intestine Large	intestine
20	chr15:41780400-41782800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:41780400-41783400	Strong transcription	Fetal Intestine Small	intestine
22	chr15:41780400-41783400	Weak transcription	Spleen	Spleen
23	chr15:41780400-41783600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:41780400-41783800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:41780400-41784000	Weak transcription	Right Ventricle	heart
26	chr15:41780400-41784600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:41780400-41784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:41780600-41782800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:41780600-41783800	Weak transcription	Gastric	stomach
30	chr15:41780600-41784600	Weak transcription	Right Atrium	heart
31	chr15:41780600-41784800	Weak transcription	Lung	lung
32	chr15:41781400-41783000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr15:41781800-41785000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:41781800-41785000	Enhancers	NHDF-Ad	bronchial
35	chr15:41781800-41785200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:41782000-41783400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr15:41782000-41783800	Enhancers	HMEC	breast
38	chr15:41782000-41784800	Enhancers	GM12878-XiMat	blood
39	chr15:41782000-41784800	Enhancers	Hela-S3	cervix
40	chr15:41782000-41784800	Enhancers	NHLF	lung
41	chr15:41782200-41783000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:41782200-41783000	Enhancers	HSMMtube	muscle
43	chr15:41782200-41783000	Enhancers	Osteobl	bone
44	chr15:41782200-41783600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:41782200-41783600	Enhancers	HSMM	muscle
46	chr15:41782200-41784000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:41782200-41785000	Enhancers	HUVEC	blood vessel
48	chr15:41782200-41785200	Enhancers	NH-A	brain
49	chr15:41782400-41783000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:41782400-41783800	Enhancers	Primary T helper cells PMA-I stimulated	--

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