Variant report

Variant	rs1389304
Chromosome Location	chr5:43039523-43039524
allele	A/G
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	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	TCF7L2	chr5:43039506-43041200	HCT-116	colon:	n/a	n/a
4	NFIC	chr5:43039379-43040920	SK-N-SH	brain:	n/a	n/a
5	EBF1	chr5:43039479-43039800	GM12878	blood:	n/a	n/a
6	REST	chr5:43039455-43041346	HL-60	blood:	n/a	chr5:43041060-43041068
7	POLR2A	chr5:43039510-43043640	K562	blood:	n/a	n/a
8	POLR2A	chr5:43039495-43040316	K562	blood:	n/a	n/a
9	RAD21	chr5:43039449-43040941	HCT-116	colon:	n/a	n/a
10	CTCF	chr5:43039460-43039730	GM12868	blood:	n/a	n/a
11	ZNF143	chr5:43039499-43041184	K562	blood:	n/a	n/a
12	TAF1	chr5:43039412-43039807	K562	blood:	n/a	n/a
13	RAD21	chr5:43039410-43040842	HCT-116	colon:	n/a	n/a
14	HEY1	chr5:43039515-43040101	HepG2	liver:	n/a	n/a
15	E2F6	chr5:43039485-43039838	K562	blood:	n/a	n/a
16	HEY1	chr5:43039506-43041259	K562	blood:	n/a	n/a
17	YY1	chr5:43039425-43040304	GM12878	blood:	n/a	chr5:43040236-43040250
18	KAP1	chr5:43039522-43040761	U2OS	brain:	n/a	n/a
19	YY1	chr5:43039488-43039845	GM12891	blood:	n/a	n/a
20	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
21	RAD21	chr5:43039510-43041187	IMR90	lung:	n/a	n/a
22	POLR2A	chr5:43039438-43040815	U87	brain:	n/a	n/a
23	MAX	chr5:43039470-43041206	K562	blood:	n/a	n/a
24	MAX	chr5:43039494-43039794	GM12878	blood:	n/a	n/a
25	BHLHE40	chr5:43039503-43040012	GM12878	blood:	n/a	n/a
26	RUNX3	chr5:43039421-43041218	GM12878	blood:	n/a	n/a
27	CTCF	chr5:43039223-43043731	A549	lung:	n/a	chr5:43041427-43041435
28	SIN3AK20	chr5:43039452-43040263	PANC-1	pancreas:	n/a	n/a
29	SIN3AK20	chr5:43039508-43040244	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr5:43039365-43041243	SK-N-SH	brain:	n/a	n/a
31	ATF2	chr5:43039421-43041278	GM12878	blood:	n/a	n/a
32	RCOR1	chr5:43039510-43041172	K562	blood:	n/a	n/a
33	MAX	chr5:43039378-43043696	A549	lung:	n/a	n/a
34	SUZ12	chr5:43039514-43041143	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr5:43039476-43041288	GM12892	blood:	n/a	n/a
36	POLR2A	chr5:43039483-43040882	HUVEC	blood vessel:	n/a	n/a
37	EP300	chr5:43039499-43042164	K562	blood:	n/a	chr5:43041260-43041274 chr5:43041356-43041370
38	STAT2	chr5:43039474-43041127	K562	blood:	n/a	chr5:43040479-43040488 chr5:43040473-43040493 chr5:43040476-43040490 chr5:43040478-43040487 chr5:43040479-43040487 chr5:43040473-43040493 chr5:43040377-43040388
39	TCF12	chr5:43039501-43039809	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr5:43039474-43043610	GM12878	blood:	n/a	n/a
41	CTCF	chr5:43039437-43040271	MCF-7	breast:	n/a	n/a
42	GATA1	chr5:43039442-43043690	PBDE	blood:	n/a	chr5:43040589-43040598
43	CTCF	chr5:43039480-43039630	GM12864	blood:	n/a	n/a
44	CTCF	chr5:43039374-43040863	HCT-116	colon:	n/a	n/a
45	MAX	chr5:43039477-43043620	NB4	blood:	n/a	n/a
46	TEAD4	chr5:43039431-43041249	K562	blood:	n/a	n/a
47	CTCF	chr5:43039488-43040255	K562	blood:	n/a	n/a
48	POLR2A	chr5:43039509-43039844	K562	blood:	n/a	n/a
49	HDAC2	chr5:43039492-43040198	MCF-7	breast:	n/a	n/a
50	IRF1	chr5:43038903-43043582	K562	blood:	n/a	chr5:43040378-43040389 chr5:43042110-43042124 chr5:43040379-43040393 chr5:43042109-43042123 chr5:43040375-43040389 chr5:43042109-43042122 chr5:43042108-43042122 chr5:43040376-43040389 chr5:43042109-43042122 chr5:43042111-43042122 chr5:43040375-43040395 chr5:43041265-43041275 chr5:43042109-43042122 chr5:43040543-43040557 chr5:43042108-43042125 chr5:43040377-43040391 chr5:43040546-43040557 chr5:43041261-43041275 chr5:43040965-43040976 chr5:43042110-43042124 chr5:43042109-43042122 chr5:43042110-43042123

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	chr5:42984356..42986139-chr5:43039157..43041117,2	K562	blood:
9	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
10	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
11	chr5:43013791..43016658-chr5:43037504..43040048,3	K562	blood:
12	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
13	chr5:42967335..42969495-chr5:43037103..43039655,2	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	chr5:43038312..43041170-chr5:43074041..43076906,4	K562	blood:
21	chr5:43005322..43013124-chr5:43037748..43043287,15	K562	blood:
22	chr5:42909164..42909729-chr5:43039167..43040032,2	K562	blood:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs4082200	1.00[YRI][hapmap]
rs55672386	1.00[AFR][1000 genomes]
rs55824534	0.88[AFR][1000 genomes]
rs56017053	1.00[AFR][1000 genomes]
rs57576393	0.81[AFR][1000 genomes]
rs58237022	1.00[AFR][1000 genomes]
rs58551906	1.00[AFR][1000 genomes]
rs58723178	0.81[AFR][1000 genomes]
rs58730711	0.88[AFR][1000 genomes]
rs61242377	1.00[AFR][1000 genomes]
rs73751007	1.00[AFR][1000 genomes]
rs73751037	0.88[AFR][1000 genomes]
rs73751040	0.81[AFR][1000 genomes]
rs73751043	0.81[AFR][1000 genomes]
rs73751302	0.88[AFR][1000 genomes]
rs73754505	0.88[AFR][1000 genomes]
rs73754508	0.88[AFR][1000 genomes]
rs73754517	0.89[AFR][1000 genomes]
rs73754520	1.00[AFR][1000 genomes]
rs73754527	1.00[AFR][1000 genomes]
rs73754531	1.00[AFR][1000 genomes]
rs73754535	1.00[AFR][1000 genomes]
rs73754536	1.00[AFR][1000 genomes]
rs73754539	1.00[AFR][1000 genomes]
rs782973	1.00[ASW][hapmap];1.00[YRI][hapmap]

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

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43035200-43039600	Weak transcription	Hela-S3	cervix
2	chr5:43036800-43039600	Active TSS	Placenta	Placenta
3	chr5:43036800-43043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:43037000-43039600	Bivalent/Poised TSS	Left Ventricle	heart
5	chr5:43037000-43040200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr5:43037000-43040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:43037000-43042200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
8	chr5:43037200-43039600	Active TSS	Muscle Satellite Cultured Cells	--
9	chr5:43037200-43040000	Active TSS	Lung	lung
10	chr5:43037200-43042400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
11	chr5:43037200-43042800	Active TSS	Right Ventricle	heart
12	chr5:43037400-43039600	Active TSS	Esophagus	oesophagus
13	chr5:43037400-43040000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr5:43037400-43043000	Active TSS	HSMM	muscle
15	chr5:43037400-43045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:43037600-43040600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:43037800-43039800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:43037800-43040200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
19	chr5:43037800-43042400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:43037800-43042800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:43037800-43042800	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr5:43037800-43043400	Active TSS	Right Atrium	heart
23	chr5:43038000-43040800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:43038000-43042600	Active TSS	Dnd41	blood
25	chr5:43038000-43043600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:43038200-43041800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr5:43038200-43042800	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr5:43038400-43040000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:43038600-43039600	Weak transcription	Gastric	stomach
30	chr5:43038600-43039600	Weak transcription	Pancreas	Pancrea
31	chr5:43038600-43039800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr5:43038600-43040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:43038600-43040200	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr5:43038600-43040400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr5:43038600-43041400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
36	chr5:43038600-43042600	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr5:43038800-43039600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:43038800-43039600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
39	chr5:43038800-43039600	Weak transcription	NHLF	lung
40	chr5:43038800-43043600	Active TSS	A549	lung
41	chr5:43039000-43039600	Active TSS	Primary T cells fromperipheralblood	blood
42	chr5:43039000-43039600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr5:43039000-43039600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:43039000-43039600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:43039000-43039600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:43039000-43039600	Active TSS	Adipose Nuclei	Adipose
47	chr5:43039000-43039600	Weak transcription	Spleen	Spleen
48	chr5:43039000-43039600	Weak transcription	HMEC	breast
49	chr5:43039000-43039600	Enhancers	NHEK	skin
50	chr5:43039000-43039800	Active TSS	Primary monocytes fromperipheralblood	blood

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