Variant report

Variant	rs9841077
Chromosome Location	chr3:51662407-51662408
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11709482	0.83[AMR][1000 genomes]
rs11719995	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4234644	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4468965	0.80[ASN][1000 genomes]
rs4494918	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864443	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864693	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866430	0.85[AMR][1000 genomes];0.81[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
rs9841077	TEX264	cis	Nerve Tibial	GTEx
rs9841077	TEX264	cis	Artery Tibial	GTEx
rs9841077	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51625400-51663400	Weak transcription	Right Ventricle	heart
2	chr3:51640600-51663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:51649800-51663400	Weak transcription	GM12878-XiMat	blood
4	chr3:51655000-51664800	Weak transcription	Fetal Kidney	kidney
5	chr3:51655400-51663200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:51655400-51664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:51655600-51662800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:51655600-51671800	Weak transcription	K562	blood
9	chr3:51655800-51664200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:51655800-51680200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:51656000-51663200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:51656000-51664000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:51656000-51669200	Weak transcription	A549	lung
14	chr3:51656000-51673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:51656400-51663200	Weak transcription	Spleen	Spleen
16	chr3:51656400-51663400	Weak transcription	Aorta	Aorta
17	chr3:51656400-51664000	Weak transcription	Small Intestine	intestine
18	chr3:51656800-51663000	Weak transcription	Hela-S3	cervix
19	chr3:51656800-51671200	Weak transcription	Stomach Mucosa	stomach
20	chr3:51657000-51663000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:51657200-51663000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:51657200-51664200	Weak transcription	Esophagus	oesophagus
23	chr3:51657200-51671200	Weak transcription	Psoas Muscle	Psoas
24	chr3:51657400-51662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:51657400-51663200	Weak transcription	HSMMtube	muscle
26	chr3:51657400-51664000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:51657400-51667200	Weak transcription	Colonic Mucosa	Colon
28	chr3:51657600-51662600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:51657600-51663200	Weak transcription	NHLF	lung
30	chr3:51657600-51664600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:51657600-51665800	Weak transcription	Fetal Brain Male	brain
32	chr3:51657600-51669000	Weak transcription	NHDF-Ad	bronchial
33	chr3:51657800-51663000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:51658600-51662600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:51659200-51662600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:51659800-51667400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:51660000-51664000	Weak transcription	NH-A	brain
38	chr3:51660000-51669600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:51660200-51664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:51660400-51665200	Weak transcription	Fetal Heart	heart
41	chr3:51660800-51666200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:51660800-51671000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:51660800-51680200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:51660800-51681000	Strong transcription	HepG2	liver
45	chr3:51660800-51681400	Strong transcription	Primary T cells from cord blood	blood
46	chr3:51660800-51681800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:51660800-51683000	Strong transcription	Primary B cells from cord blood	blood
48	chr3:51660800-51683200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:51661000-51664600	Weak transcription	HUVEC	blood vessel
50	chr3:51661000-51670600	Strong transcription	Liver	Liver

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