Variant report

Variant	rs9866051
Chromosome Location	chr3:59734687-59734688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1456154	0.92[EUR][1000 genomes]
rs1485724	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293417	0.92[EUR][1000 genomes]
rs41464544	1.00[TSI][hapmap]
rs4679503	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6785999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68003332	0.82[AMR][1000 genomes]
rs720000	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73092458	0.83[EUR][1000 genomes]
rs73092482	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092496	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73092672	0.82[AMR][1000 genomes]
rs994931	1.00[TSI][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	nsv834706	chr3:59538151-59736014	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9866051	C3orf67	cis	parietal	SCAN
rs9866051	FAM3D	cis	cerebellum	SCAN
rs9866051	DNAH12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59723000-59738600	Weak transcription	Thymus	Thymus
2	chr3:59723800-59737600	Weak transcription	Fetal Thymus	thymus
3	chr3:59730000-59738600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:59731200-59735600	Strong transcription	Primary T cells from cord blood	blood
5	chr3:59731400-59737400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:59731400-59739000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:59731800-59735200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:59732000-59737600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:59732200-59735600	Strong transcription	Dnd41	blood
10	chr3:59732400-59735600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:59732400-59736400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:59732800-59734800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:59733200-59738800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:59733200-59740200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:59734000-59734800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr3:59734000-59736400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
17	chr3:59734000-59736400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:59734000-59738000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:59734200-59734800	Enhancers	Ovary	ovary
20	chr3:59734200-59735000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:59734200-59735200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:59734200-59735400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:59734200-59736000	Enhancers	NHDF-Ad	bronchial
24	chr3:59734200-59736400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:59734200-59739800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:59734400-59735600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr3:59734400-59735800	Enhancers	Fetal Stomach	stomach
28	chr3:59734400-59735800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr3:59734400-59736400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:59734600-59735400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:59734600-59735600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:59734600-59736400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr3:59734600-59736600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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