Variant report

Variant	rs4855308
Chromosome Location	chr3:69388392-69388393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10865649	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11128126	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11707811	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1483895	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs1564757	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17005647	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872152	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2007584	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2170800	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35331889	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4290808	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4428187	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855389	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56336456	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56741529	0.85[ASN][1000 genomes]
rs59563257	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6419766	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6549198	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs6549203	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771772	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6774274	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776474	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs68061967	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611647	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7612526	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617464	0.96[ASN][1000 genomes]
rs9310148	0.96[ASN][1000 genomes]
rs9310149	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861135	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868217	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9868990	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][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	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv1800315	chr3:69374729-69414587	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4855308	FRMD4B	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69372200-69403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:69374800-69388400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:69376400-69388600	Weak transcription	Aorta	Aorta
4	chr3:69376800-69388400	Weak transcription	HSMMtube	muscle
5	chr3:69378400-69390600	Weak transcription	Thymus	Thymus
6	chr3:69378400-69400600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:69380600-69393200	Weak transcription	HSMM	muscle
8	chr3:69380800-69390600	Weak transcription	Fetal Lung	lung
9	chr3:69381200-69388400	Weak transcription	Placenta	Placenta
10	chr3:69381400-69388600	Weak transcription	Spleen	Spleen
11	chr3:69381800-69389000	Weak transcription	Lung	lung
12	chr3:69383600-69388600	Weak transcription	HUVEC	blood vessel
13	chr3:69384400-69388400	Weak transcription	Left Ventricle	heart
14	chr3:69384400-69388400	Weak transcription	Right Atrium	heart
15	chr3:69384400-69389000	Weak transcription	Brain Angular Gyrus	brain
16	chr3:69384400-69389800	Weak transcription	Brain Anterior Caudate	brain
17	chr3:69384400-69390600	Weak transcription	Fetal Heart	heart
18	chr3:69384400-69390800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:69386000-69400200	Weak transcription	NHEK	skin
20	chr3:69387200-69389000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:69387200-69389400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:69387800-69388800	Enhancers	HepG2	liver
23	chr3:69387800-69389800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:69387800-69393600	Enhancers	Brain Hippocampus Middle	brain
25	chr3:69388000-69388600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:69388000-69389000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:69388000-69389600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:69388000-69389600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:69388000-69389800	Enhancers	Primary hematopoietic stem cells	blood
30	chr3:69388000-69390000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:69388200-69389000	Enhancers	Dnd41	blood
32	chr3:69388200-69389600	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:69388200-69391800	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links