Variant report

Variant	rs4982887
Chromosome Location	chr14:24744182-24744183
allele	C/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	CEBPB	chr14:24744157-24744213	HepG2	liver:	n/a	chr14:24744166-24744177

No.	Distal block	Cell Line	Cell type
1	chr14:24742260..24745882-chr14:24750433..24756794,5	K562	blood:
2	chr14:24733261..24735631-chr14:24742751..24745334,2	K562	blood:
3	chr14:24741724..24744792-chr14:24900386..24902979,3	MCF-7	breast:
4	chr14:24743706..24746499-chr14:24758996..24760826,2	K562	blood:
5	chr14:24655787..24658216-chr14:24740858..24744211,3	K562	blood:

Variant related genes	Relation type
RABGGTA	TF binding region
ENSG00000100441	Chromatin interaction
ENSG00000092295	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000196497	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11158621	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs14193	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295313	0.85[EUR][1000 genomes]
rs3940231	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4982886	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729421	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941502	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941503	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4982887	RABGGTA	cis	multi-tissue	Pritchard
rs4982887	RABGGTA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24741200-24753200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:24741200-24758800	Weak transcription	Aorta	Aorta
3	chr14:24741200-24768200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:24741400-24744200	Enhancers	Primary B cells from peripheral blood	blood
5	chr14:24741400-24744600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr14:24741400-24744800	Enhancers	Primary B cells from cord blood	blood
7	chr14:24741400-24745200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:24741400-24745200	Enhancers	HMEC	breast
9	chr14:24741400-24746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr14:24741400-24746200	Weak transcription	Colonic Mucosa	Colon
11	chr14:24741400-24746400	Weak transcription	Right Ventricle	heart
12	chr14:24741400-24747600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:24741400-24747600	Weak transcription	Brain Substantia Nigra	brain
14	chr14:24741400-24748400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:24741400-24748400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr14:24741400-24748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:24741400-24748400	Weak transcription	Brain Angular Gyrus	brain
18	chr14:24741400-24748400	Weak transcription	Brain Anterior Caudate	brain
19	chr14:24741400-24748400	Weak transcription	Psoas Muscle	Psoas
20	chr14:24741400-24748400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr14:24741400-24748400	Weak transcription	HSMM	muscle
22	chr14:24741400-24748800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr14:24741400-24748800	Weak transcription	Lung	lung
24	chr14:24741400-24749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr14:24741400-24749800	Weak transcription	HSMMtube	muscle
26	chr14:24741400-24751800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:24741400-24752200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr14:24741400-24752200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:24741400-24757800	Weak transcription	Fetal Stomach	stomach
30	chr14:24741400-24758600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr14:24741400-24758800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr14:24741600-24744400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr14:24741600-24744800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr14:24741600-24744800	Weak transcription	Fetal Intestine Small	intestine
35	chr14:24741600-24745200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr14:24741600-24745200	Weak transcription	Brain Germinal Matrix	brain
37	chr14:24741600-24746400	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:24741600-24749600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr14:24741600-24758400	Weak transcription	Fetal Intestine Large	intestine
40	chr14:24741600-24758600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr14:24741600-24758600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr14:24741600-24759200	Weak transcription	Small Intestine	intestine
43	chr14:24741600-24767800	Weak transcription	Fetal Brain Male	brain
44	chr14:24741800-24758800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:24742000-24758600	Weak transcription	Thymus	Thymus
46	chr14:24742400-24744600	Weak transcription	Esophagus	oesophagus
47	chr14:24742800-24744400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr14:24743000-24744400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr14:24743000-24745000	Enhancers	Fetal Heart	heart
50	chr14:24743400-24744600	Weak transcription	HepG2	liver

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