Variant report

Variant	rs6860747
Chromosome Location	chr5:43039389-43039390
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	NFIC	chr5:43039379-43040920	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr5:43039223-43043731	A549	lung:	n/a	chr5:43041427-43041435
3	RAD21	chr5:43039365-43041243	SK-N-SH	brain:	n/a	n/a
4	MAX	chr5:43039378-43043696	A549	lung:	n/a	n/a
5	CTCF	chr5:43039374-43040863	HCT-116	colon:	n/a	n/a
6	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
7	CTCF	chr5:43039331-43041532	HCT-116	colon:	n/a	chr5:43041427-43041435
8	MTA3	chr5:43039375-43043696	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:43039377-43043595	HUVEC	blood vessel:	n/a	n/a
10	NFIC	chr5:43039375-43040161	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr5:43039346-43041333	PANC-1	pancreas:	n/a	n/a
12	HA-E2F1	chr5:43039358-43041357	MCF-7	breast:	n/a	chr5:43040624-43040635 chr5:43040623-43040632 chr5:43040624-43040635 chr5:43040621-43040638 chr5:43040619-43040634 chr5:43040625-43040640 chr5:43040624-43040635 chr5:43040624-43040635 chr5:43040624-43040631 chr5:43040620-43040634 chr5:43040621-43040638 chr5:43040624-43040635
13	CBX3	chr5:43039358-43041199	K562	blood:	n/a	n/a
14	POLR2A	chr5:43039343-43040869	U87	brain:	n/a	n/a
15	IRF1	chr5:43039344-43043643	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
16	POLR2A	chr5:43039279-43043734	H1-neurons	neurons:	n/a	n/a
17	SIN3AK20	chr5:43039367-43040884	MCF-7	breast:	n/a	n/a
18	SP1	chr5:43039375-43041223	A549	lung:	n/a	n/a
19	TEAD4	chr5:43039294-43043713	K562	blood:	n/a	n/a
20	TCF12	chr5:43039366-43041367	A549	lung:	n/a	chr5:43040385-43040392
21	SP1	chr5:43039319-43040866	A549	lung:	n/a	n/a
22	MYBL2	chr5:43039386-43041249	HepG2	liver:	n/a	n/a
23	CTCF	chr5:43039340-43039490	AG09319	gingival:	n/a	n/a
24	POLR2A	chr5:43039333-43043719	H1-neurons	neurons:	n/a	n/a
25	MAX	chr5:43039381-43040267	MCF-7	breast:	n/a	n/a
26	POLR2A	chr5:43039343-43040863	U87	brain:	n/a	n/a
27	MAX	chr5:43039327-43039962	MCF-7	breast:	n/a	n/a
28	MAX	chr5:43039378-43043713	A549	lung:	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	chr5:43039316..43039946-chr5:43064754..43065867,4	MCF-7	breast:
7	chr5:42984356..42986139-chr5:43039157..43041117,2	K562	blood:
8	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
9	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
10	chr5:43013791..43016658-chr5:43037504..43040048,3	K562	blood:
11	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
12	chr5:42967335..42969495-chr5:43037103..43039655,2	K562	blood:
13	chr5:43039202..43040090-chr5:43064371..43065194,2	MCF-7	breast:
14	chr5:43039238..43041150-chr5:43514128..43516342,2	K562	blood:
15	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
16	chr5:43037720..43044659-chr5:43062293..43069444,31	K562	blood:
17	chr5:43027573..43030547-chr5:43038879..43040401,2	MCF-7	breast:
18	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
19	chr5:43038312..43041170-chr5:43074041..43076906,4	K562	blood:
20	chr5:43005322..43013124-chr5:43037748..43043287,15	K562	blood:
21	chr5:42909164..42909729-chr5:43039167..43040032,2	K562	blood:

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1001718	1.00[AMR][1000 genomes]
rs10070393	1.00[AMR][1000 genomes]
rs28659803	1.00[AMR][1000 genomes]
rs3849700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55730625	1.00[AMR][1000 genomes]
rs60192164	1.00[AMR][1000 genomes]
rs60384612	1.00[AMR][1000 genomes]
rs61328340	1.00[AMR][1000 genomes]
rs6859504	1.00[AMR][1000 genomes]
rs6864556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6869639	1.00[AMR][1000 genomes]
rs6877778	1.00[AMR][1000 genomes]
rs6879509	1.00[AMR][1000 genomes]
rs6881357	1.00[AMR][1000 genomes]
rs6886169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6887110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6891509	1.00[AMR][1000 genomes]
rs6891660	1.00[AMR][1000 genomes]
rs6895975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6897663	1.00[AMR][1000 genomes]
rs73088862	1.00[AMR][1000 genomes]
rs73088863	1.00[AMR][1000 genomes]
rs73088878	1.00[AMR][1000 genomes]
rs73754524	1.00[AMR][1000 genomes]
rs73754532	1.00[AMR][1000 genomes]
rs747118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs747119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7703982	1.00[AMR][1000 genomes]
rs7710205	1.00[AMR][1000 genomes]
rs7717370	1.00[AMR][1000 genomes]
rs7718462	1.00[AMR][1000 genomes]
rs7737740	1.00[AFR][1000 genomes];1.00[AMR][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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43035200-43039600	Weak transcription	Hela-S3	cervix
2	chr5:43035800-43039400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:43036800-43039600	Active TSS	Placenta	Placenta
4	chr5:43036800-43043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:43037000-43039600	Bivalent/Poised TSS	Left Ventricle	heart
6	chr5:43037000-43040200	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr5:43037000-43040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:43037000-43042200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
9	chr5:43037200-43039600	Active TSS	Muscle Satellite Cultured Cells	--
10	chr5:43037200-43040000	Active TSS	Lung	lung
11	chr5:43037200-43042400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
12	chr5:43037200-43042800	Active TSS	Right Ventricle	heart
13	chr5:43037400-43039400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:43037400-43039600	Active TSS	Esophagus	oesophagus
15	chr5:43037400-43040000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr5:43037400-43043000	Active TSS	HSMM	muscle
17	chr5:43037400-43045000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:43037600-43040600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:43037800-43039800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:43037800-43040200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
21	chr5:43037800-43042400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:43037800-43042800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:43037800-43042800	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr5:43037800-43043400	Active TSS	Right Atrium	heart
25	chr5:43038000-43040800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:43038000-43042600	Active TSS	Dnd41	blood
27	chr5:43038000-43043600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:43038200-43041800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
29	chr5:43038200-43042800	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr5:43038400-43039400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
31	chr5:43038400-43040000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:43038600-43039400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:43038600-43039400	Bivalent/Poised TSS	Colonic Mucosa	Colon
34	chr5:43038600-43039400	Active TSS	Duodenum Mucosa	Duodenum
35	chr5:43038600-43039400	Weak transcription	HSMMtube	muscle
36	chr5:43038600-43039400	Enhancers	Osteobl	bone
37	chr5:43038600-43039600	Weak transcription	Gastric	stomach
38	chr5:43038600-43039600	Weak transcription	Pancreas	Pancrea
39	chr5:43038600-43039800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr5:43038600-43040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:43038600-43040200	Bivalent/Poised TSS	Fetal Stomach	stomach
42	chr5:43038600-43040400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr5:43038600-43041400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
44	chr5:43038600-43042600	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr5:43038800-43039400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:43038800-43039400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr5:43038800-43039600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:43038800-43039600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
49	chr5:43038800-43039600	Weak transcription	NHLF	lung
50	chr5:43038800-43043600	Active TSS	A549	lung

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