Variant report

Variant	rs4974088
Chromosome Location	chr3:48898749-48898750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10865953	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs11707968	0.90[EUR][1000 genomes]
rs12632533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap]
rs12715430	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13090141	1.00[ASN][1000 genomes]
rs13324192	1.00[ASN][1000 genomes]
rs14018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3087866	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4858800	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs4858830	1.00[CEU][hapmap]
rs4974081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs4974083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62259536	0.84[EUR][1000 genomes]
rs6442131	0.85[EUR][1000 genomes]
rs6446200	0.86[EUR][1000 genomes]
rs6446204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6766238	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs6787808	1.00[CEU][hapmap]
rs6796790	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6798112	1.00[CEU][hapmap]
rs6801211	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs7100	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7372883	0.82[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7429596	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7434187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7639370	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311431	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9864243	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs9873227	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879978	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs990211	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs4974088	GPX1	cis	parietal	SCAN
rs4974088	AMT	cis	Nerve Tibial	GTEx
rs4974088	AMT	cis	Artery Tibial	GTEx
rs4974088	AMT	cis	lymphoblastoid	seeQTL
rs4974088	TLR9	cis	parietal	SCAN
rs4974088	DALRD3	cis	cerebellum	SCAN
rs4974088	NICN1	cis	parietal	SCAN
rs4974088	PHF7	cis	parietal	SCAN
rs4974088	P4HTM	cis	lung	GTEx
rs4974088	AMT	cis	parietal	SCAN
rs4974088	NICN1	cis	cerebellum	SCAN
rs4974088	NICN1-AS1	cis	Thyroid	GTEx
rs4974088	ZNF589	cis	parietal	SCAN
rs4974088	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4974088	WDR6	cis	parietal	SCAN
rs4974088	AMT	cis	Whole Blood	GTEx
rs4974088	AMT	cis	Adipose Subcutaneous	GTEx
rs4974088	NCKIPSD	cis	parietal	SCAN
rs4974088	QRICH1	cis	cerebellum	SCAN
rs4974088	WDR6	cis	Nerve Tibial	GTEx
rs4974088	DALRD3	cis	parietal	SCAN
rs4974088	IQCF1	cis	cerebellum	SCAN
rs4974088	AMT	cis	Thyroid	GTEx
rs4974088	AMT	cis	Artery Aorta	GTEx
rs4974088	AMT	cis	Esophagus Mucosa	GTEx
rs4974088	WDR6	cis	cerebellum	SCAN
rs4974088	NICN1	cis	Thyroid	GTEx
rs4974088	P4HTM	cis	parietal	SCAN
rs4974088	LZTFL1	cis	cerebellum	SCAN
rs4974088	AMT	cis	lung	GTEx
rs4974088	WDR6	cis	Muscle Skeletal	GTEx
rs4974088	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4974088	AMT	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48885600-48915000	Weak transcription	Small Intestine	intestine
2	chr3:48885800-48899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:48885800-48900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:48885800-48906600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:48885800-48913600	Weak transcription	Fetal Lung	lung
6	chr3:48886000-48899000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:48886000-48899600	Weak transcription	NHEK	skin
8	chr3:48886000-48899800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:48886200-48900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:48886200-48900400	Weak transcription	NHLF	lung
11	chr3:48886200-48900800	Weak transcription	NHDF-Ad	bronchial
12	chr3:48886400-48899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:48886600-48901800	Weak transcription	Fetal Heart	heart
14	chr3:48889200-48902000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:48889400-48901200	Weak transcription	Fetal Brain Male	brain
16	chr3:48889600-48935400	Weak transcription	Brain Germinal Matrix	brain
17	chr3:48889800-48916800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:48891600-48904600	Weak transcription	HSMM	muscle
19	chr3:48893200-48900400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:48893200-48900600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr3:48893400-48900200	Strong transcription	Fetal Thymus	thymus
22	chr3:48893800-48900200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:48893800-48900600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:48894200-48900400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:48894400-48902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:48894400-48923000	Strong transcription	Fetal Intestine Small	intestine
27	chr3:48894600-48918800	Weak transcription	HepG2	liver
28	chr3:48894800-48899600	Weak transcription	Brain Angular Gyrus	brain
29	chr3:48895800-48900800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:48896400-48934400	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:48896600-48899200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:48896600-48918600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:48896800-48899200	Weak transcription	Placenta	Placenta
34	chr3:48896800-48899600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:48896800-48900200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:48896800-48934200	Weak transcription	Stomach Mucosa	stomach
37	chr3:48896800-48935000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:48897000-48899400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:48897000-48899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:48897000-48899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:48897000-48899600	Weak transcription	Lung	lung
42	chr3:48897000-48900800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:48897000-48911800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:48897000-48916600	Weak transcription	GM12878-XiMat	blood
45	chr3:48897000-48918400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:48897000-48918800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:48897000-48921400	Weak transcription	Primary B cells from cord blood	blood
48	chr3:48897000-48928600	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:48897000-48933600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:48897000-48934200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links