Variant report

Variant	rs12650678
Chromosome Location	chr4:56223171-56223172
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	chr4:56223124-56223393	HepG2	liver:	n/a	chr4:56223236-56223247
2	FOS	chr4:56223067-56223440	HUVEC	blood vessel:	n/a	chr4:56223236-56223247
3	POLR2A	chr4:56223030-56223636	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL1	chr4:56222902-56223521	HCT-116	colon:	n/a	n/a
5	CEBPB	chr4:56223167-56223714	MCF-7	breast:	n/a	chr4:56223453-56223464
6	ZNF217	chr4:56223023-56223700	MCF-7	breast:	n/a	n/a
7	FOSL2	chr4:56223067-56223535	HepG2	liver:	n/a	n/a
8	FOS	chr4:56223102-56223426	MCF10A-Er-Src	breast:	n/a	chr4:56223236-56223247
9	FOXA1	chr4:56223136-56223700	HepG2	liver:	n/a	n/a
10	CEBPB	chr4:56223164-56223727	MCF-7	breast:	n/a	chr4:56223453-56223464
11	NR3C1	chr4:56223079-56223723	A549	lung:	n/a	chr4:56223574-56223588 chr4:56223573-56223589 chr4:56223571-56223592 chr4:56223573-56223590 chr4:56223573-56223589 chr4:56223574-56223588 chr4:56223574-56223588 chr4:56223570-56223591 chr4:56223573-56223589 chr4:56223573-56223589
12	JUND	chr4:56223003-56223721	SK-N-SH	brain:	n/a	chr4:56223236-56223247
13	JUND	chr4:56223055-56223437	Hela-S3	cervix:	n/a	chr4:56223236-56223247
14	JUND	chr4:56223047-56223416	K562	blood:	n/a	chr4:56223236-56223247
15	NR3C1	chr4:56223166-56223743	A549	lung:	n/a	chr4:56223574-56223588 chr4:56223573-56223589 chr4:56223571-56223592 chr4:56223573-56223590 chr4:56223573-56223589 chr4:56223574-56223588 chr4:56223574-56223588 chr4:56223570-56223591 chr4:56223573-56223589 chr4:56223573-56223589
16	HA-E2F1	chr4:56222629-56223646	MCF-7	breast:	n/a	n/a
17	NR2F2	chr4:56223052-56223728	MCF-7	breast:	n/a	n/a
18	JUND	chr4:56223084-56223398	HepG2	liver:	n/a	chr4:56223236-56223247
19	TBL1XR1	chr4:56223161-56223345	K562	blood:	n/a	n/a
20	FOXA2	chr4:56223064-56223679	A549	lung:	n/a	n/a
21	FOXA1	chr4:56223155-56223653	A549	lung:	n/a	n/a
22	MYC	chr4:56223027-56223585	MCF10A-Er-Src	breast:	n/a	n/a
23	CEBPB	chr4:56223124-56223646	Hela-S3	cervix:	n/a	chr4:56223453-56223464
24	FOXA1	chr4:56223116-56223693	A549	lung:	n/a	n/a
25	FOS	chr4:56223054-56223509	MCF10A-Er-Src	breast:	n/a	chr4:56223236-56223247
26	FOXA2	chr4:56223082-56223675	HepG2	liver:	n/a	n/a
27	FOSL2	chr4:56223007-56223487	HepG2	liver:	n/a	n/a
28	FOS	chr4:56223054-56223495	MCF10A-Er-Src	breast:	n/a	chr4:56223236-56223247
29	JUN	chr4:56223153-56223380	HepG2	liver:	n/a	n/a
30	FOXA1	chr4:56223158-56223599	HepG2	liver:	n/a	n/a
31	FOXA1	chr4:56223167-56223696	HepG2	liver:	n/a	n/a
32	FOSL2	chr4:56222994-56223546	MCF-7	breast:	n/a	n/a
33	JUN	chr4:56223111-56223320	K562	blood:	n/a	n/a
34	FOS	chr4:56223046-56223424	MCF10A-Er-Src	breast:	n/a	chr4:56223236-56223247
35	FOSL2	chr4:56223082-56223462	A549	lung:	n/a	n/a
36	TCF7L2	chr4:56223098-56223540	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
2	chr4:56220332..56223664-chr4:56260663..56265029,5	K562	blood:
3	chr4:56217456..56218965-chr4:56223007..56224946,2	MCF-7	breast:
4	chr4:56222589..56224784-chr4:56242075..56244451,2	K562	blood:
5	chr4:56221079..56223378-chr4:56272404..56274272,2	MCF-7	breast:
6	chr4:56209954..56216628-chr4:56219638..56226284,12	MCF-7	breast:
7	chr4:56217504..56220153-chr4:56221676..56223372,2	MCF-7	breast:
8	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
9	chr4:56223084..56223996-chr4:56259734..56260367,2	MCF-7	breast:
10	chr4:56221889..56224651-chr4:56225282..56227252,2	K562	blood:

Variant related genes	Relation type
FCF1P8	TF binding region
SRD5A3	TF binding region
ENSG00000249700	Chromatin interaction
ENSG00000251111	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000128039	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10001859	0.81[EUR][1000 genomes]
rs11133375	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124164	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133010	0.80[ASN][1000 genomes]
rs13138693	0.81[ASN][1000 genomes]
rs1985606	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2063577	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4864982	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305114	0.81[ASN][1000 genomes]
rs6813878	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6835891	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7664100	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672248	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9790808	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12650678	TMEM165	cis	Nerve Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213200-56230000	Weak transcription	Fetal Kidney	kidney
2	chr4:56213400-56223800	Weak transcription	Fetal Heart	heart
3	chr4:56213400-56225400	Weak transcription	Spleen	Spleen
4	chr4:56213400-56233600	Weak transcription	Fetal Intestine Large	intestine
5	chr4:56213600-56224000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:56213600-56225600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:56213600-56229200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:56213600-56230200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:56213600-56230200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:56213600-56242600	Weak transcription	Gastric	stomach
11	chr4:56213800-56225200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:56213800-56225600	Weak transcription	Left Ventricle	heart
13	chr4:56213800-56227000	Weak transcription	Placenta	Placenta
14	chr4:56213800-56229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:56213800-56229800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:56213800-56229800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:56213800-56231800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:56213800-56233600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
20	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
21	chr4:56214000-56223400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:56214000-56224600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:56214000-56225600	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:56214000-56229800	Weak transcription	Liver	Liver
25	chr4:56214000-56229800	Weak transcription	Fetal Thymus	thymus
26	chr4:56214000-56229800	Weak transcription	Thymus	Thymus
27	chr4:56214000-56230200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:56214000-56231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:56214000-56237800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
31	chr4:56214200-56224800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:56214600-56224200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr4:56214600-56230200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:56214800-56225000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:56215000-56223400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:56215000-56224200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:56215000-56224400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:56215000-56225400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:56215000-56227400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:56215000-56229800	Weak transcription	Brain Angular Gyrus	brain
42	chr4:56215000-56235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:56215200-56225000	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:56218800-56225200	Weak transcription	Brain Substantia Nigra	brain
45	chr4:56219200-56224600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:56219200-56224800	Weak transcription	Brain Anterior Caudate	brain
47	chr4:56219200-56230000	Weak transcription	Fetal Lung	lung
48	chr4:56219400-56238400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:56219600-56224800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:56219600-56229800	Weak transcription	Dnd41	blood

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