Variant report

Variant	rs56399450
Chromosome Location	chr3:112283375-112283376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112281323..112284151-chr3:113775113..113776995,2	K562	blood:
2	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
3	chr3:112280159..112284151-chr3:113775113..113778230,3	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction
ENSG00000151576	Chromatin interaction
ENSG00000163617	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1980049	1.00[AMR][1000 genomes]
rs55689097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56253335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56683778	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57472957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57496061	0.88[AFR][1000 genomes]
rs73853442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73853914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73853926	1.00[AMR][1000 genomes]
rs73853927	1.00[AMR][1000 genomes]
rs73855812	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112278600-112283800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr3:112281800-112283800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:112281800-112286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:112281800-112287000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:112281800-112289800	Weak transcription	HSMMtube	muscle
6	chr3:112281800-112290400	Weak transcription	Lung	lung
7	chr3:112281800-112291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
9	chr3:112281800-112301600	Weak transcription	HepG2	liver
10	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
12	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
13	chr3:112281800-112325400	Weak transcription	Gastric	stomach
14	chr3:112282000-112284000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:112282000-112285200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:112282000-112287200	Weak transcription	Aorta	Aorta
17	chr3:112282000-112288200	Weak transcription	Ovary	ovary
18	chr3:112282000-112289600	Weak transcription	Colonic Mucosa	Colon
19	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
22	chr3:112282200-112283400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:112282200-112284200	Weak transcription	Fetal Thymus	thymus
24	chr3:112282200-112284400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:112282200-112284800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:112282200-112285200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:112282200-112286400	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:112282200-112287200	Weak transcription	HSMM	muscle
29	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
30	chr3:112282400-112283600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:112282400-112283600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:112282400-112283800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:112282400-112283800	Weak transcription	Liver	Liver
34	chr3:112282400-112284200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112282400-112284600	Enhancers	Fetal Intestine Large	intestine
36	chr3:112282400-112284600	Enhancers	Fetal Intestine Small	intestine
37	chr3:112282400-112286000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:112282400-112286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:112282400-112287000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:112282400-112287400	Weak transcription	NH-A	brain
41	chr3:112282400-112287400	Weak transcription	Osteobl	bone
42	chr3:112282400-112288200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:112282400-112289000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:112282400-112289200	Weak transcription	Brain Substantia Nigra	brain
45	chr3:112282400-112289800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:112282400-112290400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:112282400-112290400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:112282400-112291200	Weak transcription	NHLF	lung
49	chr3:112282400-112291800	Weak transcription	Fetal Kidney	kidney
50	chr3:112282400-112299400	Weak transcription	Fetal Stomach	stomach

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