Variant report

Variant	rs1423458
Chromosome Location	chr5:108064681-108064682
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	IRF1	chr5:108063820-108064814	K562	blood:	n/a	chr5:108064309-108064323 chr5:108064744-108064758 chr5:108064431-108064445 chr5:108064310-108064320 chr5:108064742-108064756 chr5:108064309-108064323 chr5:108064281-108064295 chr5:108064310-108064323 chr5:108064740-108064754
2	POLR2A	chr5:108062323-108064800	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:108062196-108064794	K562	blood:	n/a	n/a
4	POLR2A	chr5:108062392-108064816	U87	brain:	n/a	n/a
5	MYC	chr5:108062898-108064790	NB4	blood:	n/a	chr5:108064303-108064312
6	EP300	chr5:108063853-108064893	GM12878	blood:	n/a	chr5:108064551-108064565
7	RCOR1	chr5:108062183-108064863	K562	blood:	n/a	n/a
8	CHD2	chr5:108063320-108064721	GM12878	blood:	n/a	n/a
9	JUND	chr5:108062208-108064888	K562	blood:	n/a	chr5:108064436-108064445 chr5:108064437-108064446
10	POLR2A	chr5:108064522-108064759	GM12891	blood:	n/a	n/a
11	POLR2A	chr5:108062961-108064755	GM12878	blood:	n/a	n/a
12	STAT3	chr5:108064633-108064833	Hela-S3	cervix:	n/a	chr5:108064744-108064755 chr5:108064718-108064725
13	TBL1XR1	chr5:108063360-108064883	GM12878	blood:	n/a	n/a
14	MYC	chr5:108063903-108065201	MCF10A-Er-Src	breast:	n/a	chr5:108064303-108064312
15	ATF2	chr5:108063132-108064870	GM12878	blood:	n/a	n/a
16	EP300	chr5:108063858-108064806	GM12878	blood:	n/a	chr5:108064551-108064565
17	CEBPB	chr5:108063229-108065583	Hela-S3	cervix:	n/a	chr5:108065188-108065201 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065138-108065147 chr5:108065188-108065199 chr5:108065136-108065147 chr5:108065188-108065201 chr5:108065138-108065147 chr5:108065138-108065147
18	POLR2A	chr5:108063109-108064853	Hela-S3	cervix:	n/a	n/a
19	MYC	chr5:108062249-108064878	K562	blood:	n/a	chr5:108064303-108064312
20	POLR2A	chr5:108061807-108064833	K562	blood:	n/a	n/a
21	MXI1	chr5:108062860-108064966	SK-N-SH	brain:	n/a	n/a
22	SMARCC1	chr5:108063016-108064960	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:108062883-108064839	GM12878	blood:	n/a	n/a
24	EP300	chr5:108062212-108065250	K562	blood:	n/a	chr5:108064551-108064565 chr5:108065056-108065070 chr5:108063707-108063716
25	ARID3A	chr5:108064639-108065280	K562	blood:	n/a	n/a
26	POLR2A	chr5:108062550-108064818	GM19099	blood:	n/a	n/a
27	POLR2A	chr5:108062363-108064709	K562	blood:	n/a	n/a
28	RCOR1	chr5:108064664-108065347	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr5:108062340-108065386	K562	blood:	n/a	chr5:108065188-108065201 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065138-108065147 chr5:108065188-108065199 chr5:108065136-108065147 chr5:108065188-108065201 chr5:108065138-108065147 chr5:108065138-108065147
30	FOXM1	chr5:108063349-108064774	GM12878	blood:	n/a	n/a
31	POLR2A	chr5:108062960-108064771	GM18526	blood:	n/a	n/a
32	MTA3	chr5:108062082-108064854	GM12878	blood:	n/a	n/a
33	RUNX3	chr5:108062977-108064844	GM12878	blood:	n/a	n/a
34	FOXM1	chr5:108063792-108064831	GM12878	blood:	n/a	n/a
35	CEBPB	chr5:108063162-108065377	A549	lung:	n/a	chr5:108065188-108065201 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065138-108065147 chr5:108065188-108065199 chr5:108065136-108065147 chr5:108065188-108065201 chr5:108065138-108065147 chr5:108065138-108065147
36	POLR2A	chr5:108062851-108064729	K562	blood:	n/a	n/a
37	RELA	chr5:108063881-108064698	GM10847	blood:	n/a	n/a
38	PML	chr5:108062820-108064761	GM12878	blood:	n/a	n/a
39	ELF1	chr5:108064510-108064757	K562	blood:	n/a	n/a
40	CREB1	chr5:108063192-108064915	GM12878	blood:	n/a	n/a
41	MXI1	chr5:108063826-108064771	K562	blood:	n/a	n/a
42	POLR2A	chr5:108062119-108064828	PBDE	blood:	n/a	n/a
43	POLR2A	chr5:108064514-108064878	GM12891	blood:	n/a	n/a
44	ZNF143	chr5:108064651-108064685	Hela-S3	cervix:	n/a	n/a
45	MAX	chr5:108062444-108064838	NB4	blood:	n/a	chr5:108064303-108064312
46	MYC	chr5:108062960-108065027	MCF10A-Er-Src	breast:	n/a	chr5:108064303-108064312
47	RCOR1	chr5:108063058-108064758	K562	blood:	n/a	n/a
48	ZNF263	chr5:108062994-108064816	HEK293-T-REx	kidney:	n/a	n/a
49	CREB1	chr5:108063407-108065060	K562	blood:	n/a	n/a
50	NR2F2	chr5:108063134-108064989	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:108060235..108074407-chr5:108078172..108087811,48	K562	blood:
2	chr5:108062598..108065696-chr5:108743430..108747045,3	K562	blood:
3	chr5:108062273..108066431-chr5:108081834..108086243,5	MCF-7	breast:
4	chr5:108062575..108065883-chr5:108081229..108085721,5	MCF-7	breast:
5	chr5:108063588..108065189-chr5:109024997..109026908,2	MCF-7	breast:
6	chr5:108059312..108068052-chr5:108079113..108087366,42	K562	blood:

Variant related genes	Relation type
LINC01023	TF binding region
ENSG00000198961	Chromatin interaction
ENSG00000112893	Chromatin interaction
ENSG00000151422	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1423455	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56366803	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57331813	1.00[AMR][1000 genomes]
rs6594339	1.00[AMR][1000 genomes]
rs6879203	1.00[AMR][1000 genomes]
rs73780552	1.00[AMR][1000 genomes]
rs73780554	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7714960	1.00[AMR][1000 genomes]
rs7719100	1.00[AMR][1000 genomes]
rs7734770	1.00[AMR][1000 genomes]
rs7736849	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1423458	NEFH	trans	lymphoblastoid	seeQTL
rs1423458	FKBP7	trans	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108062200-108065000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:108062400-108065000	Active TSS	Brain Hippocampus Middle	brain
3	chr5:108062600-108064800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:108062600-108065000	Active TSS	Stomach Smooth Muscle	stomach
5	chr5:108062800-108064800	Active TSS	Aorta	Aorta
6	chr5:108062800-108064800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr5:108062800-108065000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:108062800-108065000	Active TSS	Brain Anterior Caudate	brain
9	chr5:108062800-108065000	Active TSS	Brain Cingulate Gyrus	brain
10	chr5:108062800-108065000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr5:108062800-108065000	Active TSS	Right Atrium	heart
12	chr5:108062800-108065000	Active TSS	K562	blood
13	chr5:108063000-108064800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:108063000-108064800	Active TSS	Psoas Muscle	Psoas
15	chr5:108063000-108064800	Flanking Active TSS	Dnd41	blood
16	chr5:108063200-108064800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr5:108063200-108064800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:108063200-108064800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:108063200-108064800	Active TSS	Brain Substantia Nigra	brain
20	chr5:108063200-108064800	Active TSS	Fetal Brain Female	brain
21	chr5:108063200-108064800	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr5:108063200-108065000	Active TSS	Ovary	ovary
23	chr5:108063200-108065200	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr5:108063200-108065400	Active TSS	Fetal Brain Male	brain
25	chr5:108063400-108064800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:108063400-108064800	Active TSS	Thymus	Thymus
27	chr5:108063400-108064800	Active TSS	GM12878-XiMat	blood
28	chr5:108063400-108065000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:108063400-108065600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr5:108063600-108065000	Active TSS	Rectal Smooth Muscle	rectum
31	chr5:108063600-108065000	Active TSS	Osteobl	bone
32	chr5:108063600-108065200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr5:108064200-108064800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr5:108064200-108064800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr5:108064200-108064800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr5:108064200-108064800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr5:108064200-108064800	Flanking Active TSS	HSMMtube	muscle
38	chr5:108064200-108064800	Flanking Active TSS	HUVEC	blood vessel
39	chr5:108064200-108065000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr5:108064200-108065000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr5:108064200-108065000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr5:108064200-108065200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr5:108064200-108065200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr5:108064200-108065200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:108064200-108065200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:108064200-108065400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr5:108064400-108064800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:108064400-108064800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:108064400-108064800	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr5:108064400-108064800	Flanking Active TSS	Brain Germinal Matrix	brain

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