Variant report

Variant	rs3822296
Chromosome Location	chr4:15416824-15416825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10002931	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003338	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032941	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212901	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024758	0.81[CEU][hapmap]
rs1048037	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10488970	0.84[EUR][1000 genomes]
rs11934015	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937671	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233742	0.84[EUR][1000 genomes]
rs13106702	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114788	0.84[EUR][1000 genomes]
rs13123785	0.80[CEU][hapmap]
rs13124324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124984	0.83[EUR][1000 genomes]
rs13131227	0.86[CHD][hapmap]
rs13132007	0.84[EUR][1000 genomes]
rs13132446	0.84[EUR][1000 genomes]
rs13132604	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs13138481	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs16891929	0.81[EUR][1000 genomes]
rs16891934	0.81[EUR][1000 genomes]
rs1990524	0.83[EUR][1000 genomes]
rs2160043	0.84[JPT][hapmap]
rs2160046	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2192355	0.83[EUR][1000 genomes]
rs2192363	0.85[ASN][1000 genomes]
rs2192364	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215810	0.85[ASN][1000 genomes]
rs28376639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872704	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34028526	0.84[EUR][1000 genomes]
rs34351987	0.84[EUR][1000 genomes]
rs34352292	0.84[EUR][1000 genomes]
rs35866305	0.84[EUR][1000 genomes]
rs35971217	0.84[EUR][1000 genomes]
rs3797006	0.81[CEU][hapmap]
rs4140932	0.86[ASN][1000 genomes]
rs59684117	0.84[EUR][1000 genomes]
rs61240629	0.84[EUR][1000 genomes]
rs62289285	0.84[EUR][1000 genomes]
rs6449138	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855244	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71601473	0.83[EUR][1000 genomes]
rs7442554	0.83[EUR][1000 genomes]
rs7661287	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681816	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690471	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697778	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973629	0.85[ASN][1000 genomes]
rs9991652	0.97[AMR][1000 genomes];0.99[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3822296	SLC39A8	trans	cerebellum	SCAN
rs3822296	HS3ST1	cis	parietal	SCAN
rs3822296	CPEB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15405400-15422000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:15407600-15418000	Weak transcription	Left Ventricle	heart
3	chr4:15411000-15417200	Enhancers	Primary B cells from peripheral blood	blood
4	chr4:15411200-15419800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:15411400-15418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:15411400-15418600	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:15412400-15421800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:15412600-15421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:15412800-15420800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:15413000-15419400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr4:15413200-15418000	Weak transcription	Right Atrium	heart
12	chr4:15413600-15418000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:15413600-15418000	Weak transcription	Spleen	Spleen
14	chr4:15414600-15417000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:15414600-15417000	Enhancers	Osteobl	bone
16	chr4:15414800-15417000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:15414800-15417000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:15414800-15417000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr4:15414800-15417200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:15415200-15417000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr4:15415200-15417000	Enhancers	Fetal Stomach	stomach
22	chr4:15415200-15417200	Enhancers	NHDF-Ad	bronchial
23	chr4:15415200-15417800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:15415800-15417600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:15416000-15417000	Enhancers	Rectal Smooth Muscle	rectum
26	chr4:15416200-15417000	Enhancers	HSMM	muscle
27	chr4:15416200-15417600	Enhancers	Primary B cells from cord blood	blood
28	chr4:15416200-15418000	Weak transcription	Aorta	Aorta
29	chr4:15416400-15417800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:15416400-15417800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr4:15416400-15418000	Weak transcription	Fetal Thymus	thymus
32	chr4:15416400-15419000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:15416400-15419400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:15416600-15418200	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:15416600-15419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:15416800-15417000	Enhancers	Small Intestine	intestine
37	chr4:15416800-15417800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:15416800-15417800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:15416800-15418000	Weak transcription	Fetal Heart	heart
40	chr4:15416800-15418000	Weak transcription	Ovary	ovary
41	chr4:15416800-15418200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:15416800-15421800	Weak transcription	NHLF	lung
43	chr4:15416800-15422000	Weak transcription	Brain Substantia Nigra	brain
44	chr4:15416800-15422000	Weak transcription	HSMMtube	muscle
45	chr4:15416800-15422000	Weak transcription	NH-A	brain
46	chr4:15416800-15429000	Weak transcription	Fetal Lung	lung

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