Variant report

Variant	rs12653983
Chromosome Location	chr5:7852978-7852979
allele	A/C
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	EBF1	chr5:7852556-7853201	GM12878	blood:	n/a	chr5:7852652-7852665 chr5:7852654-7852663 chr5:7852654-7852664
2	EBF1	chr5:7852846-7853106	GM12878	blood:	n/a	n/a
3	IRF1	chr5:7852833-7853096	K562	blood:	n/a	chr5:7852984-7852998 chr5:7852986-7852998 chr5:7852983-7852997 chr5:7852987-7852997 chr5:7852985-7852998 chr5:7852987-7852998 chr5:7852986-7853003 chr5:7852988-7852999 chr5:7852985-7852998 chr5:7852985-7852998 chr5:7852984-7853001
4	TBL1XR1	chr5:7852890-7853062	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7849253..7853514-chr5:7868734..7871211,5	MCF-7	breast:

Variant related genes	Relation type
C5orf49	TF binding region
ENSG00000124275	Chromatin interaction
ENSG00000124279	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1005101	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1108209	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1563911	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1993716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1993717	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57110438	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57580763	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73737638	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7714950	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv461927	chr5:7757812-7854289	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv597004	chr5:7757812-7854289	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7851000-7853000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:7851200-7859600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:7851400-7853200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr5:7851400-7857800	Weak transcription	Left Ventricle	heart
5	chr5:7851400-7858000	Weak transcription	HSMM	muscle
6	chr5:7851400-7859600	Weak transcription	Esophagus	oesophagus
7	chr5:7851400-7860000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:7851600-7853400	Enhancers	Fetal Lung	lung
9	chr5:7851600-7853400	Enhancers	Ovary	ovary
10	chr5:7851600-7857000	Weak transcription	Fetal Stomach	stomach
11	chr5:7851600-7857600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:7851600-7857600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:7851600-7857600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:7851600-7857600	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:7851600-7857800	Weak transcription	Brain Angular Gyrus	brain
16	chr5:7851600-7857800	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:7851600-7857800	Weak transcription	Fetal Intestine Large	intestine
18	chr5:7851600-7858000	Weak transcription	Adipose Nuclei	Adipose
19	chr5:7851600-7858200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:7851600-7859000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:7851600-7859200	Weak transcription	Fetal Brain Female	brain
22	chr5:7851600-7859800	Weak transcription	Psoas Muscle	Psoas
23	chr5:7851600-7859800	Weak transcription	Right Ventricle	heart
24	chr5:7851600-7860000	Weak transcription	Aorta	Aorta
25	chr5:7851600-7861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:7851600-7861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:7851600-7865000	Weak transcription	Small Intestine	intestine
28	chr5:7851600-7866400	Weak transcription	Fetal Heart	heart
29	chr5:7851800-7853000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr5:7851800-7857800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:7851800-7859200	Weak transcription	HMEC	breast
32	chr5:7851800-7859600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:7851800-7861800	Weak transcription	Brain Substantia Nigra	brain
34	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:7852000-7853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:7852000-7857600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:7852200-7853000	Enhancers	Liver	Liver
38	chr5:7852200-7853400	Enhancers	Stomach Smooth Muscle	stomach
39	chr5:7852200-7858000	Weak transcription	A549	lung
40	chr5:7852200-7858200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:7852200-7867600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:7852200-7868400	Weak transcription	Gastric	stomach
45	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:7852400-7854800	Weak transcription	Brain Germinal Matrix	brain
47	chr5:7852400-7857600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:7852400-7859600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:7852400-7859800	Weak transcription	Spleen	Spleen
50	chr5:7852400-7861000	Weak transcription	HepG2	liver

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