Variant report

Variant	rs28919899
Chromosome Location	chr5:42806345-42806346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:42806093-42807039	HepG2	liver:	n/a	n/a
2	HEY1	chr5:42805975-42809968	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:42806127-42806410	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:42806105-42806836	HepG2	liver:	n/a	n/a
5	HEY1	chr5:42806025-42806428	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:42806062-42807231	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:42805758-42812555	HepG2	liver:	n/a	n/a
8	MBD4	chr5:42804512-42808794	HepG2	liver:	n/a	n/a
9	CTCF	chr5:42806200-42806350	NHLF	lung:	n/a	n/a
10	POLR2A	chr5:42797012-42808716	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:42798272-42812268	HepG2	liver:	n/a	n/a
12	MYBL2	chr5:42805714-42807317	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42804005..42807710-chr5:42809581..42813463,4	K562	blood:
2	chr5:42804005..42807994-chr5:42809581..42813463,4	K562	blood:

No data

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

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10038990	1.00[ASN][1000 genomes]
rs10045847	1.00[ASN][1000 genomes]
rs10045863	1.00[ASN][1000 genomes]
rs10056315	1.00[ASN][1000 genomes]
rs10067153	1.00[ASN][1000 genomes]
rs10069861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10070118	1.00[ASN][1000 genomes]
rs10070249	1.00[ASN][1000 genomes]
rs10072083	1.00[ASN][1000 genomes]
rs10072749	1.00[ASN][1000 genomes]
rs1105983	1.00[ASN][1000 genomes]
rs11951328	1.00[ASN][1000 genomes]
rs13168440	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171019	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13171505	1.00[ASN][1000 genomes]
rs13172646	1.00[ASN][1000 genomes]
rs13187223	1.00[ASN][1000 genomes]
rs13189374	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081164	1.00[ASN][1000 genomes]
rs28705009	1.00[ASN][1000 genomes]
rs28919913	1.00[ASN][1000 genomes]
rs34086275	1.00[ASN][1000 genomes]
rs34829612	1.00[ASN][1000 genomes]
rs34831882	1.00[ASN][1000 genomes]
rs35904649	1.00[ASN][1000 genomes]
rs3877899	1.00[ASN][1000 genomes]
rs4283796	1.00[ASN][1000 genomes]
rs4866943	0.81[EUR][1000 genomes]
rs5025611	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6413428	1.00[ASN][1000 genomes]
rs6451633	0.80[EUR][1000 genomes]
rs6451634	0.81[EUR][1000 genomes]
rs6451635	0.81[EUR][1000 genomes]
rs6863953	1.00[ASN][1000 genomes]
rs6869224	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6873794	0.81[EUR][1000 genomes]
rs6878461	0.81[EUR][1000 genomes]
rs6894403	0.89[EUR][1000 genomes]
rs6896899	1.00[ASN][1000 genomes]
rs71627561	1.00[ASN][1000 genomes]
rs7447731	0.81[EUR][1000 genomes]
rs7710105	1.00[ASN][1000 genomes]
rs7722920	1.00[ASN][1000 genomes]
rs9292859	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42788600-42807600	Weak transcription	Primary T cells from cord blood	blood
2	chr5:42789600-42813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:42791400-42811200	Weak transcription	Fetal Thymus	thymus
4	chr5:42792000-42807600	Weak transcription	NHDF-Ad	bronchial
5	chr5:42795600-42810200	Weak transcription	Thymus	Thymus
6	chr5:42797000-42810600	Weak transcription	Esophagus	oesophagus
7	chr5:42797400-42810800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:42797600-42808200	Weak transcription	HSMM	muscle
9	chr5:42797800-42809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:42798200-42808400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:42798200-42811200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:42798600-42808200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:42798800-42806400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
15	chr5:42799400-42807000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:42799400-42807400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:42799400-42808200	Weak transcription	Colonic Mucosa	Colon
18	chr5:42799600-42807600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:42799600-42811400	Weak transcription	Fetal Brain Female	brain
20	chr5:42799600-42812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:42799800-42807400	Strong transcription	Adipose Nuclei	Adipose
22	chr5:42799800-42808200	Strong transcription	Placenta	Placenta
23	chr5:42799800-42808400	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:42800000-42808200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:42800000-42809400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:42800400-42806600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:42800600-42807200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:42800600-42808000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:42800600-42811200	Weak transcription	Small Intestine	intestine
30	chr5:42800800-42806800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:42800800-42808200	Weak transcription	Stomach Mucosa	stomach
32	chr5:42801400-42806400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:42802000-42809000	Weak transcription	Right Ventricle	heart
34	chr5:42802000-42809600	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:42802000-42810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:42802000-42810200	Weak transcription	Brain Germinal Matrix	brain
37	chr5:42802000-42810600	Weak transcription	Aorta	Aorta
38	chr5:42802000-42810600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:42802000-42810600	Weak transcription	Gastric	stomach
40	chr5:42802000-42810600	Weak transcription	Lung	lung
41	chr5:42802000-42811000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:42802000-42811200	Weak transcription	Spleen	Spleen
43	chr5:42802200-42810200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:42802400-42808200	Weak transcription	Psoas Muscle	Psoas
45	chr5:42802400-42810600	Weak transcription	Pancreas	Pancrea
46	chr5:42802400-42810800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:42803600-42806800	Strong transcription	Left Ventricle	heart
48	chr5:42803800-42806800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:42803800-42810800	Weak transcription	Fetal Brain Male	brain
50	chr5:42804000-42806800	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links