Variant report

Variant	rs4928098
Chromosome Location	chr3:100214084-100214085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100213098..100216032-chr3:100220024..100221553,2	K562	blood:
2	chr3:100212615..100215029-chr3:100245878..100248398,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11920006	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923942	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11926280	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11927516	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12636805	0.94[ASN][1000 genomes]
rs12639465	0.81[JPT][hapmap]
rs4132537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928097	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs58059387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59299896	0.96[ASN][1000 genomes]
rs59771628	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60071944	0.96[ASN][1000 genomes]
rs62276520	0.96[ASN][1000 genomes]
rs62276521	0.96[ASN][1000 genomes]
rs62276522	0.92[ASN][1000 genomes]
rs62276523	0.92[ASN][1000 genomes]
rs62276526	0.88[ASN][1000 genomes]
rs62276527	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441285	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441300	0.82[JPT][hapmap]
rs6763079	0.93[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs6763178	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs67774605	0.96[ASN][1000 genomes]
rs6789867	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73152126	0.90[ASN][1000 genomes]
rs7430698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7430715	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7616839	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7619507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630198	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640470	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7653196	0.82[JPT][hapmap]
rs9813069	0.84[ASN][1000 genomes]
rs9851429	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4928098	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs4928098	TMEM45A	cis	multi-tissue	Pritchard
rs4928098	TMEM45A	cis	lymphoblastoid	seeQTL
rs4928098	IMPG2	cis	cerebellum	SCAN
rs4928098	COL8A1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100212000-100215400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:100212000-100215800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:100212200-100215600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:100212400-100214400	Weak transcription	NHDF-Ad	bronchial
5	chr3:100212400-100214800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:100212400-100214800	Weak transcription	NHEK	skin
7	chr3:100212400-100215200	Weak transcription	HSMMtube	muscle
8	chr3:100212400-100215200	Weak transcription	NH-A	brain
9	chr3:100212400-100215200	Weak transcription	NHLF	lung
10	chr3:100212400-100215400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:100212400-100215600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:100212400-100219200	Weak transcription	Aorta	Aorta
13	chr3:100212400-100222800	Weak transcription	Ovary	ovary
14	chr3:100212600-100214800	Weak transcription	HMEC	breast
15	chr3:100212600-100215200	Weak transcription	Osteobl	bone
16	chr3:100212600-100215400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:100212800-100214400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:100212800-100214800	Weak transcription	HSMM	muscle
19	chr3:100212800-100215200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:100212800-100217800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:100212800-100224800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:100213200-100215000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:100213200-100216400	Weak transcription	Fetal Stomach	stomach
24	chr3:100213400-100217600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:100213600-100214200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:100213600-100215200	Enhancers	HepG2	liver
27	chr3:100213800-100214400	Enhancers	Lung	lung
28	chr3:100213800-100215400	Enhancers	Liver	Liver
29	chr3:100213800-100216000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:100214000-100214200	Enhancers	Duodenum Mucosa	Duodenum
31	chr3:100214000-100214400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:100214000-100214400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:100214000-100214800	Enhancers	GM12878-XiMat	blood
34	chr3:100214000-100215200	Weak transcription	Brain Anterior Caudate	brain
35	chr3:100214000-100215200	Weak transcription	Spleen	Spleen
36	chr3:100214000-100223600	Weak transcription	Fetal Lung	lung

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