Variant report

Variant	rs6809155
Chromosome Location	chr3:51623216-51623217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1055429	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130293	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11719995	0.82[EUR][1000 genomes]
rs11721253	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3821829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4067	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4234644	1.00[CEU][hapmap]
rs4317086	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4355273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs4611808	0.86[AMR][1000 genomes]
rs4687568	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687569	0.84[AMR][1000 genomes]
rs4687721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687734	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6445791	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6771081	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6771491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6775666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6787312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6793900	0.86[AMR][1000 genomes]
rs7372658	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9311469	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9866430	0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6809155	TEX264	cis	Esophagus Muscularis	GTEx
rs6809155	TEX264	cis	Artery Tibial	GTEx
rs6809155	TEX264	cis	Esophagus Mucosa	GTEx
rs6809155	TEX264	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:51574800-51624800	Weak transcription	NH-A	brain
4	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
5	chr3:51585200-51624400	Weak transcription	Brain Germinal Matrix	brain
6	chr3:51585800-51625000	Weak transcription	Colonic Mucosa	Colon
7	chr3:51587800-51624400	Weak transcription	Hela-S3	cervix
8	chr3:51588000-51640000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:51600800-51654600	Weak transcription	Stomach Mucosa	stomach
10	chr3:51601000-51624600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:51601200-51640000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:51602800-51624400	Weak transcription	NHLF	lung
13	chr3:51602800-51628200	Weak transcription	Small Intestine	intestine
14	chr3:51602800-51643800	Weak transcription	Right Atrium	heart
15	chr3:51603200-51624400	Weak transcription	Right Ventricle	heart
16	chr3:51607600-51624600	Weak transcription	GM12878-XiMat	blood
17	chr3:51607800-51624400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:51607800-51624400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:51607800-51624400	Weak transcription	Placenta	Placenta
20	chr3:51612800-51624400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:51613200-51624200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:51613200-51624400	Weak transcription	Primary B cells from cord blood	blood
23	chr3:51613200-51624400	Weak transcription	Fetal Brain Female	brain
24	chr3:51613200-51629400	Weak transcription	Fetal Lung	lung
25	chr3:51613200-51630800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:51613200-51640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:51613400-51624400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:51613400-51624400	Weak transcription	Ovary	ovary
29	chr3:51613400-51624400	Weak transcription	Spleen	Spleen
30	chr3:51613400-51643600	Weak transcription	Pancreas	Pancrea
31	chr3:51614400-51624200	Weak transcription	Thymus	Thymus
32	chr3:51614400-51624400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:51614400-51626600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:51614600-51624200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:51614600-51624400	Weak transcription	Fetal Intestine Large	intestine
36	chr3:51614600-51624400	Weak transcription	Gastric	stomach
37	chr3:51614800-51624400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:51615000-51624400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:51615600-51623800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:51615600-51624600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:51615800-51625000	Weak transcription	NHDF-Ad	bronchial
42	chr3:51615800-51630800	Weak transcription	Psoas Muscle	Psoas
43	chr3:51616000-51624200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:51616000-51624200	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:51616000-51624400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:51616000-51624600	Weak transcription	Fetal Heart	heart
47	chr3:51616000-51624600	Weak transcription	HSMMtube	muscle
48	chr3:51616200-51624400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:51616200-51624600	Weak transcription	Osteobl	bone
50	chr3:51616400-51624400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links