Variant report

Variant	rs4928097
Chromosome Location	chr3:100213778-100213779
allele	C/T
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: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11920006	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11923942	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926280	0.87[ASN][1000 genomes]
rs11927516	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631075	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12634371	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12636452	0.91[MEX][hapmap]
rs12636805	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639465	0.89[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs4132537	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4928098	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4928110	0.91[MEX][hapmap]
rs4928111	0.81[AMR][1000 genomes]
rs57018910	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58059387	0.96[ASN][1000 genomes]
rs58789183	0.81[AMR][1000 genomes]
rs59299896	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59771628	0.96[ASN][1000 genomes]
rs60071944	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60272820	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61636409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62276517	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62276520	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276521	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276522	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62276523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62276526	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276527	0.87[ASN][1000 genomes]
rs62276556	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62276559	0.89[EUR][1000 genomes]
rs6441285	0.88[ASN][1000 genomes]
rs6441300	0.82[JPT][hapmap]
rs66791174	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67600559	0.95[EUR][1000 genomes]
rs6763079	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763178	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67774605	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789867	0.96[ASN][1000 genomes]
rs6798264	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73152126	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7429072	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7429277	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7429604	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7430698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7431846	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7619507	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7630198	0.96[ASN][1000 genomes]
rs7653196	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs9813069	0.83[ASN][1000 genomes]
rs9851429	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4928097	TMEM45A	cis	Whole Blood	GTEx
rs4928097	TMEM45A	cis	parietal	SCAN
rs4928097	OR5K4	cis	cerebellum	SCAN
rs4928097	TMEM45A	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100211000-100214000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:100211800-100213800	Weak transcription	Lung	lung
3	chr3:100212000-100215400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:100212000-100215800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:100212200-100215600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:100212400-100214000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:100212400-100214400	Weak transcription	NHDF-Ad	bronchial
8	chr3:100212400-100214800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:100212400-100214800	Weak transcription	NHEK	skin
10	chr3:100212400-100215200	Weak transcription	HSMMtube	muscle
11	chr3:100212400-100215200	Weak transcription	NH-A	brain
12	chr3:100212400-100215200	Weak transcription	NHLF	lung
13	chr3:100212400-100215400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:100212400-100215600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:100212400-100219200	Weak transcription	Aorta	Aorta
16	chr3:100212400-100222800	Weak transcription	Ovary	ovary
17	chr3:100212600-100214800	Weak transcription	HMEC	breast
18	chr3:100212600-100215200	Weak transcription	Osteobl	bone
19	chr3:100212600-100215400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:100212800-100214400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:100212800-100214800	Weak transcription	HSMM	muscle
22	chr3:100212800-100215200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:100212800-100217800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:100212800-100224800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:100213200-100215000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:100213200-100216400	Weak transcription	Fetal Stomach	stomach
27	chr3:100213400-100214000	Enhancers	Fetal Lung	lung
28	chr3:100213400-100217600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:100213600-100213800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:100213600-100213800	Flanking Active TSS	Liver	Liver
31	chr3:100213600-100214000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:100213600-100214000	Enhancers	Brain Anterior Caudate	brain
33	chr3:100213600-100214000	Enhancers	Spleen	Spleen
34	chr3:100213600-100214000	Flanking Active TSS	GM12878-XiMat	blood
35	chr3:100213600-100214200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:100213600-100215200	Enhancers	HepG2	liver

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