Variant report

Variant	rs1054428
Chromosome Location	chr5:43039793-43039794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:242)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:242 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr5:43039441-43039877	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr5:43039469-43039839	GM12878	blood:	n/a	n/a
3	ATF3	chr5:43039572-43040251	A549	lung:	n/a	n/a
4	POLR2A	chr5:43039619-43040295	GM12891	blood:	n/a	n/a
5	PML	chr5:43039608-43043658	K562	blood:	n/a	n/a
6	CTCF	chr5:43039760-43039910	RPTEC	kidney:	n/a	n/a
7	TCF7L2	chr5:43039506-43041200	HCT-116	colon:	n/a	n/a
8	NFIC	chr5:43039379-43040920	SK-N-SH	brain:	n/a	n/a
9	EBF1	chr5:43039479-43039800	GM12878	blood:	n/a	n/a
10	REST	chr5:43039455-43041346	HL-60	blood:	n/a	chr5:43041060-43041068
11	POLR2A	chr5:43039510-43043640	K562	blood:	n/a	n/a
12	POLR2A	chr5:43039495-43040316	K562	blood:	n/a	n/a
13	MTA3	chr5:43039726-43041182	GM12878	blood:	n/a	n/a
14	GTF2B	chr5:43039649-43040158	K562	blood:	n/a	n/a
15	POLR2A	chr5:43039532-43043686	PBDE	blood:	n/a	n/a
16	RAD21	chr5:43039449-43040941	HCT-116	colon:	n/a	n/a
17	ZNF143	chr5:43039499-43041184	K562	blood:	n/a	n/a
18	TAF1	chr5:43039412-43039807	K562	blood:	n/a	n/a
19	RAD21	chr5:43039410-43040842	HCT-116	colon:	n/a	n/a
20	HEY1	chr5:43039515-43040101	HepG2	liver:	n/a	n/a
21	TBP	chr5:43039536-43043625	K562	blood:	n/a	n/a
22	E2F6	chr5:43039485-43039838	K562	blood:	n/a	n/a
23	HEY1	chr5:43039506-43041259	K562	blood:	n/a	n/a
24	CHD2	chr5:43039582-43039851	K562	blood:	n/a	n/a
25	YY1	chr5:43039425-43040304	GM12878	blood:	n/a	chr5:43040236-43040250
26	KAP1	chr5:43039522-43040761	U2OS	brain:	n/a	n/a
27	YY1	chr5:43039488-43039845	GM12891	blood:	n/a	n/a
28	STAT1	chr5:43039520-43043515	Hela-S3	cervix:	n/a	chr5:43040479-43040488 chr5:43040473-43040493 chr5:43040476-43040490 chr5:43042111-43042122 chr5:43040478-43040487 chr5:43040479-43040487 chr5:43040477-43040488 chr5:43040473-43040493 chr5:43040377-43040388
29	RAD21	chr5:43039510-43041187	IMR90	lung:	n/a	n/a
30	POLR2A	chr5:43039438-43040815	U87	brain:	n/a	n/a
31	EBF1	chr5:43039584-43041531	GM12878	blood:	n/a	n/a
32	CEBPB	chr5:43039612-43041058	A549	lung:	n/a	chr5:43040604-43040615 chr5:43040137-43040148
33	MAX	chr5:43039470-43041206	K562	blood:	n/a	n/a
34	MAX	chr5:43039494-43039794	GM12878	blood:	n/a	n/a
35	BHLHE40	chr5:43039503-43040012	GM12878	blood:	n/a	n/a
36	NR2F2	chr5:43039783-43040795	K562	blood:	n/a	n/a
37	RUNX3	chr5:43039421-43041218	GM12878	blood:	n/a	n/a
38	CTCF	chr5:43039223-43043731	A549	lung:	n/a	chr5:43041427-43041435
39	CTCF	chr5:43039554-43039801	MCF-7	breast:	n/a	n/a
40	POLR2A	chr5:43039535-43040257	MCF-7	breast:	n/a	n/a
41	POLR2A	chr5:43039622-43039931	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr5:43039452-43040263	PANC-1	pancreas:	n/a	n/a
43	SIN3AK20	chr5:43039508-43040244	SK-N-SH	brain:	n/a	n/a
44	RAD21	chr5:43039365-43041243	SK-N-SH	brain:	n/a	n/a
45	YY1	chr5:43039563-43039891	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr5:43039572-43040216	MCF-7	breast:	n/a	n/a
47	MYC	chr5:43039604-43039798	MCF-7	breast:	n/a	n/a
48	ATF2	chr5:43039421-43041278	GM12878	blood:	n/a	n/a
49	RCOR1	chr5:43039510-43041172	K562	blood:	n/a	n/a
50	MAX	chr5:43039378-43043696	A549	lung:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43005892..43011349-chr5:43037590..43043804,20	K562	blood:
2	chr5:42909052..42909674-chr5:43039401..43040103,2	MCF-7	breast:
3	chr5:43034026..43036831-chr5:43037498..43040104,5	MCF-7	breast:
4	chr5:43013791..43017090-chr5:43037504..43040048,4	K562	blood:
5	chr5:42907582..42909644-chr5:43037324..43039921,2	K562	blood:
6	chr5:42911247..42912986-chr5:43038290..43040466,2	MCF-7	breast:
7	chr5:43039316..43039946-chr5:43064754..43065867,4	MCF-7	breast:
8	chr5:43018166..43019016-chr5:43039659..43040518,2	MCF-7	breast:
9	chr5:42984356..42986139-chr5:43039157..43041117,2	K562	blood:
10	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
11	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
12	chr5:43013791..43016658-chr5:43037504..43040048,3	K562	blood:
13	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
14	chr5:43039202..43040090-chr5:43064371..43065194,2	MCF-7	breast:
15	chr5:43039238..43041150-chr5:43514128..43516342,2	K562	blood:
16	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
17	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
18	chr5:43027573..43030547-chr5:43038879..43040401,2	MCF-7	breast:
19	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
20	chr5:43019736..43020278-chr5:43039607..43040176,2	MCF-7	breast:
21	chr5:43038312..43041170-chr5:43074041..43076906,4	K562	blood:
22	chr5:43005322..43013124-chr5:43037748..43043287,15	K562	blood:
23	chr5:42909164..42909729-chr5:43039167..43040032,2	K562	blood:
24	chr5:43007330..43009530-chr5:43039640..43043303,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215068	TF binding region
ENSG00000271788	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000251131	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000272144	Chromatin interaction
ENSG00000251656	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10941609	1.00[CHD][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap]
rs11746055	1.00[CHD][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap]
rs11748652	1.00[CHD][hapmap]
rs12110174	1.00[CHD][hapmap]
rs12514198	1.00[CHD][hapmap]
rs1845485	1.00[CHD][hapmap]
rs35137321	1.00[ASN][1000 genomes]
rs4637560	1.00[ASN][1000 genomes]
rs550400	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58933160	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
9	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
10	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1054428	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43036800-43043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:43037000-43040200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr5:43037000-43040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:43037000-43042200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
5	chr5:43037200-43040000	Active TSS	Lung	lung
6	chr5:43037200-43042400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr5:43037200-43042800	Active TSS	Right Ventricle	heart
8	chr5:43037400-43040000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr5:43037400-43043000	Active TSS	HSMM	muscle
10	chr5:43037400-43045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:43037600-43040600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:43037800-43039800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:43037800-43040200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr5:43037800-43042400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:43037800-43042800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:43037800-43042800	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr5:43037800-43043400	Active TSS	Right Atrium	heart
18	chr5:43038000-43040800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:43038000-43042600	Active TSS	Dnd41	blood
20	chr5:43038000-43043600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:43038200-43041800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr5:43038200-43042800	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr5:43038400-43040000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:43038600-43039800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr5:43038600-43040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:43038600-43040200	Bivalent/Poised TSS	Fetal Stomach	stomach
27	chr5:43038600-43040400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr5:43038600-43041400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
29	chr5:43038600-43042600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr5:43038800-43043600	Active TSS	A549	lung
31	chr5:43039000-43039800	Active TSS	Primary monocytes fromperipheralblood	blood
32	chr5:43039000-43040000	Active TSS	Fetal Thymus	thymus
33	chr5:43039000-43041400	Active TSS	Primary B cells from peripheral blood	blood
34	chr5:43039000-43041400	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr5:43039000-43042800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr5:43039000-43042800	Active TSS	GM12878-XiMat	blood
37	chr5:43039000-43042800	Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:43039000-43043600	Active TSS	Psoas Muscle	Psoas
39	chr5:43039000-43043800	Active TSS	Thymus	Thymus
40	chr5:43039000-43043800	Active TSS	NHDF-Ad	bronchial
41	chr5:43039200-43039800	Active TSS	HUVEC	blood vessel
42	chr5:43039200-43040600	Active TSS	Primary T cells from cord blood	blood
43	chr5:43039200-43041600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr5:43039200-43042600	Active TSS	K562	blood
45	chr5:43039400-43039800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
46	chr5:43039400-43039800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
47	chr5:43039400-43039800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:43039400-43039800	Bivalent/Poised TSS	Liver	Liver
49	chr5:43039400-43039800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
50	chr5:43039400-43039800	Flanking Active TSS	Osteobl	bone

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