Variant report

Variant	rs9866430
Chromosome Location	chr3:51591265-51591266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1055429	0.84[EUR][1000 genomes]
rs11709482	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164599	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4234644	0.89[EUR][1000 genomes]
rs4494918	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687721	0.84[EUR][1000 genomes]
rs6809155	0.82[EUR][1000 genomes]
rs7625821	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9841077	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9864443	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9864693	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9866430	TEX264	cis	Esophagus Muscularis	GTEx
rs9866430	TEX264	cis	Nerve Tibial	GTEx
rs9866430	TEX264	cis	Artery Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51573800-51594000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:51574000-51593800	Weak transcription	Right Ventricle	heart
3	chr3:51574000-51597000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:51574000-51600600	Weak transcription	Gastric	stomach
5	chr3:51574000-51615400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:51574200-51616400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:51574400-51593200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:51574400-51613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:51574600-51593200	Weak transcription	Brain Anterior Caudate	brain
11	chr3:51574600-51593200	Weak transcription	NHLF	lung
12	chr3:51574600-51593400	Weak transcription	HSMMtube	muscle
13	chr3:51574600-51593800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:51574600-51593800	Weak transcription	Left Ventricle	heart
15	chr3:51574600-51594400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:51574600-51600800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:51574600-51601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:51574800-51597600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:51574800-51624800	Weak transcription	NH-A	brain
21	chr3:51575000-51597400	Weak transcription	Small Intestine	intestine
22	chr3:51575200-51615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:51575600-51593200	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:51576000-51595400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:51576200-51593000	Strong transcription	Fetal Stomach	stomach
26	chr3:51576400-51593200	Weak transcription	HSMM	muscle
27	chr3:51576400-51597800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:51576400-51602000	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:51577200-51597600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:51578600-51591400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:51578600-51607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:51578800-51593400	Weak transcription	NHDF-Ad	bronchial
33	chr3:51578800-51597400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:51578800-51600200	Weak transcription	A549	lung
35	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
36	chr3:51579000-51593600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:51579000-51602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:51579200-51602400	Weak transcription	HMEC	breast
39	chr3:51580000-51602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:51583800-51591600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:51584200-51600200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:51584200-51602200	Weak transcription	Pancreas	Pancrea
43	chr3:51584200-51602200	Weak transcription	Spleen	Spleen
44	chr3:51584200-51614200	Weak transcription	Aorta	Aorta
45	chr3:51584400-51592800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:51584400-51593400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:51584600-51592000	Weak transcription	Ovary	ovary
48	chr3:51584600-51597000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:51584800-51593200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:51584800-51593800	Weak transcription	HepG2	liver

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