Variant report

Variant	rs316396
Chromosome Location	chr5:43038959-43038960
allele	G/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	chr5:43038903-43043582	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
2	YY1	chr5:43038608-43038975	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:43037897-43039072	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr5:43038816-43039159	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr5:43038026-43039068	HL-60	blood:	n/a	n/a
6	RCOR1	chr5:43036862-43039162	IMR90	lung:	n/a	n/a
7	POLR2A	chr5:43036710-43039237	H1-neurons	neurons:	n/a	n/a
8	MTA3	chr5:43037784-43039044	GM12878	blood:	n/a	n/a
9	MAX	chr5:43038516-43039039	K562	blood:	n/a	n/a
10	TEAD4	chr5:43037808-43039115	K562	blood:	n/a	n/a
11	POLR2A	chr5:43037889-43039063	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43005892..43011349-chr5:43037590..43043804,20	K562	blood:
2	chr5:43034026..43036831-chr5:43037498..43040104,5	MCF-7	breast:
3	chr5:43013791..43017090-chr5:43037504..43040048,4	K562	blood:
4	chr5:42907582..42909644-chr5:43037324..43039921,2	K562	blood:
5	chr5:42911247..42912986-chr5:43038290..43040466,2	MCF-7	breast:
6	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
7	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
8	chr5:43013791..43016658-chr5:43037504..43040048,3	K562	blood:
9	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
10	chr5:42967335..42969495-chr5:43037103..43039655,2	K562	blood:
11	chr5:43038347..43039048-chr5:43105566..43106088,2	MCF-7	breast:
12	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
13	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
14	chr5:43027573..43030547-chr5:43038879..43040401,2	MCF-7	breast:
15	chr5:43036891..43039253-chr5:43074561..43077276,2	MCF-7	breast:
16	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
17	chr5:43038312..43041170-chr5:43074041..43076906,4	K562	blood:
18	chr5:43005322..43013124-chr5:43037748..43043287,15	K562	blood:
19	chr5:43008478..43012422-chr5:43036002..43039064,3	MCF-7	breast:

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

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10522	0.90[ASN][1000 genomes]
rs10941604	0.81[ASN][1000 genomes]
rs10941605	0.81[ASN][1000 genomes]
rs11747435	0.81[ASN][1000 genomes]
rs11958008	0.81[ASN][1000 genomes]
rs12697439	0.87[ASN][1000 genomes]
rs13169690	0.90[ASN][1000 genomes]
rs13170208	0.86[ASN][1000 genomes]
rs13178479	0.86[ASN][1000 genomes]
rs1542369	0.85[ASN][1000 genomes]
rs1574407	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs160709	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs178415	0.87[ASN][1000 genomes]
rs1902101	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2124069	0.82[ASN][1000 genomes]
rs222060	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2253450	0.81[ASN][1000 genomes]
rs2329994	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2329995	0.87[ASN][1000 genomes]
rs2548353	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2548356	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2603295	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2603636	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2603656	0.81[ASN][1000 genomes]
rs309909	0.81[AFR][1000 genomes]
rs309914	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs316395	0.92[ASN][1000 genomes]
rs316400	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316402	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316403	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316404	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316406	0.84[ASN][1000 genomes]
rs316408	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316413	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316414	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs316416	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs316419	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs316422	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4033115	0.86[ASN][1000 genomes]
rs4092293	0.90[ASN][1000 genomes]
rs4092294	0.90[ASN][1000 genomes]
rs4296812	0.81[ASN][1000 genomes]
rs515970	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543569	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565761	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs613825	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs643307	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6451660	0.86[ASN][1000 genomes]
rs6451661	0.86[ASN][1000 genomes]
rs6451662	0.86[ASN][1000 genomes]
rs6875214	0.89[ASN][1000 genomes]
rs724430	0.85[ASN][1000 genomes]
rs768441	0.90[ASN][1000 genomes]
rs7715065	0.83[ASN][1000 genomes]
rs9292862	0.88[AFR][1000 genomes];0.92[ASN][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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43035200-43039600	Weak transcription	Hela-S3	cervix
2	chr5:43035600-43039200	Weak transcription	HepG2	liver
3	chr5:43035800-43039400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:43036800-43039000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr5:43036800-43039600	Active TSS	Placenta	Placenta
6	chr5:43036800-43043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:43037000-43039000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr5:43037000-43039000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr5:43037000-43039000	Flanking Active TSS	NHEK	skin
10	chr5:43037000-43039600	Bivalent/Poised TSS	Left Ventricle	heart
11	chr5:43037000-43040200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr5:43037000-43040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:43037000-43042200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
14	chr5:43037200-43039000	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr5:43037200-43039600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr5:43037200-43040000	Active TSS	Lung	lung
17	chr5:43037200-43042400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
18	chr5:43037200-43042800	Active TSS	Right Ventricle	heart
19	chr5:43037400-43039000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr5:43037400-43039400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:43037400-43039600	Active TSS	Esophagus	oesophagus
22	chr5:43037400-43040000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr5:43037400-43043000	Active TSS	HSMM	muscle
24	chr5:43037400-43045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:43037600-43039000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr5:43037600-43039000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
27	chr5:43037600-43039000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr5:43037600-43039200	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr5:43037600-43040600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:43037800-43039800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:43037800-43040200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
32	chr5:43037800-43042400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:43037800-43042800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:43037800-43042800	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr5:43037800-43043400	Active TSS	Right Atrium	heart
36	chr5:43038000-43039200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr5:43038000-43040800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:43038000-43042600	Active TSS	Dnd41	blood
39	chr5:43038000-43043600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:43038200-43039000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:43038200-43039000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:43038200-43039000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr5:43038200-43039000	Flanking Active TSS	Thymus	Thymus
44	chr5:43038200-43039200	Flanking Active TSS	K562	blood
45	chr5:43038200-43041800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
46	chr5:43038200-43042800	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr5:43038400-43039000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
48	chr5:43038400-43039000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr5:43038400-43039000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:43038400-43039000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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