Variant report

Variant	rs278373
Chromosome Location	chr3:98453951-98453952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs115931	0.96[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs278363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278370	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278374	0.82[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3755569	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7611040	0.81[JPT][hapmap]
rs7634817	0.83[MEX][hapmap]
rs828589	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828593	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828594	0.82[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828595	0.96[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs828596	0.82[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828597	0.82[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828598	0.82[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs828599	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs828602	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828613	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs844159	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs844161	0.85[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs865474	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs893831	0.82[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs893832	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9879927	0.80[CHD][hapmap];0.82[JPT][hapmap]

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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv470783	chr3:98431225-98466222	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs278373	ST3GAL6-AS1	cis	Heart Left Ventricle	GTEx
rs278373	OR5K1	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98450600-98454000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:98450600-98454200	Active TSS	Fetal Kidney	kidney
3	chr3:98450600-98455600	Active TSS	GM12878-XiMat	blood
4	chr3:98450800-98454000	Active TSS	Right Ventricle	heart
5	chr3:98452200-98455000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:98452400-98454000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:98453000-98454400	Flanking Active TSS	Liver	Liver
8	chr3:98453000-98454800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98453000-98456800	Weak transcription	Esophagus	oesophagus
10	chr3:98453000-98459200	Weak transcription	Pancreas	Pancrea
11	chr3:98453200-98454800	Weak transcription	Lung	lung
12	chr3:98453400-98454000	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:98453400-98454000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:98453400-98454000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:98453400-98454000	Enhancers	Fetal Brain Male	brain
16	chr3:98453400-98454000	Enhancers	Placenta	Placenta
17	chr3:98453400-98454200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:98453400-98454200	Enhancers	Brain Substantia Nigra	brain
19	chr3:98453400-98454200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:98453400-98454200	Enhancers	Dnd41	blood
21	chr3:98453400-98454600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:98453400-98456600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:98453400-98458200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr3:98453400-98460200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:98453400-98463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:98453400-98463400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:98453400-98468600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:98453400-98469400	Weak transcription	Aorta	Aorta
29	chr3:98453600-98454000	Flanking Active TSS	Left Ventricle	heart
30	chr3:98453600-98454200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:98453600-98454200	Flanking Active TSS	Fetal Brain Female	brain
32	chr3:98453600-98454400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:98453600-98454800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:98453600-98454800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:98453800-98454000	Enhancers	Fetal Thymus	thymus
36	chr3:98453800-98454000	Active TSS	Thymus	Thymus
37	chr3:98453800-98454200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:98453800-98454200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:98453800-98454200	Flanking Active TSS	Right Atrium	heart
40	chr3:98453800-98454200	Enhancers	HUVEC	blood vessel
41	chr3:98453800-98454400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:98453800-98455200	Enhancers	Fetal Heart	heart
43	chr3:98453800-98456400	Enhancers	HepG2	liver
44	chr3:98453800-98459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:98453800-98459800	Weak transcription	HMEC	breast
46	chr3:98453800-98464200	Weak transcription	Brain Hippocampus Middle	brain

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