Variant report

Variant	rs4306902
Chromosome Location	chr3:191118258-191118259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1435059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1435063	0.84[ASN][1000 genomes]
rs2028572	0.81[EUR][1000 genomes]
rs2028574	0.81[EUR][1000 genomes]
rs4677728	0.81[EUR][1000 genomes]
rs4677729	0.81[EUR][1000 genomes]
rs4677730	0.81[EUR][1000 genomes]
rs9827755	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised 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	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4306902	CCDC50	cis	Nerve Tibial	GTEx
rs4306902	CCDC50	cis	Artery Aorta	GTEx
rs4306902	CCDC50	cis	Thyroid	GTEx
rs4306902	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
3	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
6	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
8	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
10	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
11	chr3:191100200-191119600	Weak transcription	K562	blood
12	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
13	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
14	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
15	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
17	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:191112200-191118400	Strong transcription	NH-A	brain
20	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:191114200-191119200	Weak transcription	Fetal Intestine Large	intestine
22	chr3:191114200-191119400	Weak transcription	NHLF	lung
23	chr3:191114400-191119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:191114400-191119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:191114400-191120400	Weak transcription	HSMM	muscle
26	chr3:191114400-191121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:191114400-191121400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:191116000-191119800	Weak transcription	Left Ventricle	heart
29	chr3:191116000-191119800	Weak transcription	Ovary	ovary
30	chr3:191116000-191121200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:191116000-191121600	Weak transcription	Primary B cells from cord blood	blood
32	chr3:191116400-191118800	Weak transcription	Placenta	Placenta
33	chr3:191116600-191118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:191116600-191118800	Weak transcription	Osteobl	bone
35	chr3:191116600-191119600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:191116600-191119600	Weak transcription	Liver	Liver
37	chr3:191117000-191118600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:191117000-191118600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:191117200-191127200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:191117200-191127200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:191117400-191118400	ZNF genes & repeats	Lung	lung
42	chr3:191117800-191118400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr3:191117800-191118400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:191117800-191118400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:191117800-191119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:191118000-191119800	Weak transcription	Adipose Nuclei	Adipose
47	chr3:191118000-191121000	Weak transcription	HUVEC	blood vessel
48	chr3:191118200-191120000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:191118200-191127200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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