Variant report

Variant	rs28919886
Chromosome Location	chr5:42811450-42811451
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	NFIC	chr5:42810738-42812636	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:42811408-42811498	HepG2	liver:	n/a	n/a
3	ESRRA	chr5:42811426-42813042	GM12878	blood:	n/a	chr5:42812084-42812094 chr5:42812074-42812092
4	HEY1	chr5:42810042-42812656	HepG2	liver:	n/a	n/a
5	HEY1	chr5:42810707-42812193	HepG2	liver:	n/a	n/a
6	REST	chr5:42811102-42812422	HepG2	liver:	n/a	chr5:42811432-42811452 chr5:42811433-42811451 chr5:42811694-42811712
7	MBD4	chr5:42810705-42812670	HepG2	liver:	n/a	n/a
8	FOXA2	chr5:42811420-42812691	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:42811230-42812202	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:42805758-42812555	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:42811209-42812189	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:42811164-42812402	MCF10A-Er-Src	breast:	n/a	n/a
13	MBD4	chr5:42810669-42812631	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:42810152-42812313	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:42810832-42812567	HepG2	liver:	n/a	n/a
16	MYBL2	chr5:42810747-42812749	HepG2	liver:	n/a	n/a
17	MYBL2	chr5:42811262-42812676	HepG2	liver:	n/a	n/a
18	POLR2A	chr5:42798272-42812268	HepG2	liver:	n/a	n/a
19	POLR2A	chr5:42810756-42812217	HepG2	liver:	n/a	n/a
20	TBP	chr5:42811356-42812533	HepG2	liver:	n/a	n/a
21	POLR2A	chr5:42811239-42812521	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:42804005..42807710-chr5:42809581..42813463,4	K562	blood:
2	chr5:42804005..42807994-chr5:42809581..42813463,4	K562	blood:
3	chr5:42808126..42809697-chr5:42810037..42813024,2	K562	blood:

Variant related genes	Relation type
SEPP1	TF binding region
ENSG00000250722	Chromatin interaction
ENSG00000272234	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6874738	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6890032	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42789600-42813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
3	chr5:42799600-42812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:42807600-42812600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr5:42807800-42812800	Active TSS	Right Atrium	heart
6	chr5:42808000-42812600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr5:42808200-42812200	Active TSS	Duodenum Mucosa	Duodenum
8	chr5:42808200-42812600	Active TSS	Colonic Mucosa	Colon
9	chr5:42808400-42811600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:42808400-42812400	Active TSS	Brain Cingulate Gyrus	brain
11	chr5:42808400-42812400	Active TSS	Brain Substantia Nigra	brain
12	chr5:42808400-42812400	Active TSS	Placenta	Placenta
13	chr5:42808400-42812600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:42808400-42812600	Active TSS	Ovary	ovary
15	chr5:42808400-42812600	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr5:42808600-42811800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:42808600-42812400	Active TSS	Liver	Liver
18	chr5:42808600-42812400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr5:42808600-42812600	Active TSS	Psoas Muscle	Psoas
20	chr5:42808800-42812200	Active TSS	Colon Smooth Muscle	Colon
21	chr5:42809000-42812400	Active TSS	Fetal Intestine Small	intestine
22	chr5:42809000-42812400	Active TSS	Right Ventricle	heart
23	chr5:42809200-42812600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr5:42809200-42812600	Active TSS	Stomach Smooth Muscle	stomach
25	chr5:42809400-42812400	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr5:42809400-42812600	Active TSS	Fetal Stomach	stomach
27	chr5:42809400-42812800	Active TSS	Brain Angular Gyrus	brain
28	chr5:42809600-42812000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:42809600-42812400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:42809600-42812400	Active TSS	Fetal Muscle Leg	muscle
31	chr5:42809600-42812400	Active TSS	Rectal Smooth Muscle	rectum
32	chr5:42809600-42812400	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr5:42809600-42812800	Active TSS	Brain Anterior Caudate	brain
34	chr5:42809600-42812800	Active TSS	Brain Hippocampus Middle	brain
35	chr5:42809800-42812000	Active TSS	Fetal Lung	lung
36	chr5:42809800-42812200	Active TSS	Adipose Nuclei	Adipose
37	chr5:42809800-42812400	Active TSS	Fetal Intestine Large	intestine
38	chr5:42810000-42812000	Active TSS	Fetal Kidney	kidney
39	chr5:42810200-42811800	Active TSS	Thymus	Thymus
40	chr5:42810200-42812600	Active TSS	Brain Germinal Matrix	brain
41	chr5:42810200-42812600	Active TSS	NHDF-Ad	bronchial
42	chr5:42810400-42812200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr5:42810400-42812600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:42810600-42811600	Active TSS	Gastric	stomach
45	chr5:42810600-42811800	Active TSS	Esophagus	oesophagus
46	chr5:42810600-42811800	Active TSS	Lung	lung
47	chr5:42810600-42811800	Active TSS	Pancreas	Pancrea
48	chr5:42810600-42812200	Active TSS	Aorta	Aorta
49	chr5:42810600-42812200	Active TSS	Left Ventricle	heart
50	chr5:42810600-42812200	Active TSS	NHLF	lung

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