Variant report

Variant	rs6772668
Chromosome Location	chr3:51460426-51460427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1031925	0.91[CEU][hapmap]
rs11130290	0.81[ASN][1000 genomes]
rs12632046	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1383251	0.91[CEU][hapmap]
rs1480353	0.91[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1542574	0.91[CEU][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1552074	1.00[CEU][hapmap]
rs17051762	0.83[CEU][hapmap]
rs2127655	0.83[CEU][hapmap]
rs2164599	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219890	0.91[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241784	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687569	0.81[EUR][1000 genomes]
rs4687721	0.91[CEU][hapmap]
rs4687800	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974104	0.91[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974105	0.91[CEU][hapmap]
rs6445620	0.91[CEU][hapmap]
rs6445622	0.91[CEU][hapmap]
rs6445628	0.91[CEU][hapmap]
rs6445727	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774745	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6787312	0.92[CEU][hapmap]
rs751075	0.91[CEU][hapmap]
rs7617533	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623803	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7625006	0.91[CEU][hapmap]
rs7625821	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633708	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7640083	0.81[ASN][1000 genomes]
rs7648012	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7649069	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv3369762	chr3:51449727-51469314	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3444499	chr3:51449727-51469614	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6772668	TEX264	cis	Nerve Tibial	GTEx
rs6772668	TEX264	cis	Artery Tibial	GTEx
rs6772668	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51431400-51471200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:51433400-51477400	Weak transcription	Fetal Heart	heart
3	chr3:51434000-51475600	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr3:51434200-51477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:51434600-51471000	Weak transcription	Stomach Mucosa	stomach
6	chr3:51435200-51478000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:51436600-51461000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:51436800-51461000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:51439800-51478000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:51440800-51478200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:51441600-51461400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:51444000-51460600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:51444000-51461200	Strong transcription	Placenta	Placenta
14	chr3:51444800-51477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:51445400-51478400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:51446000-51460600	Strong transcription	Fetal Thymus	thymus
17	chr3:51446000-51460800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:51446200-51460600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:51446200-51471000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:51446400-51461000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:51446400-51461200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:51446400-51461200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:51446400-51461200	Strong transcription	Thymus	Thymus
24	chr3:51448800-51462000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:51449600-51461000	Strong transcription	Fetal Brain Female	brain
26	chr3:51449800-51460800	Strong transcription	GM12878-XiMat	blood
27	chr3:51451200-51476800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:51451400-51469600	Strong transcription	Fetal Stomach	stomach
29	chr3:51452400-51463200	Strong transcription	Fetal Intestine Small	intestine
30	chr3:51454000-51467400	Weak transcription	Small Intestine	intestine
31	chr3:51454800-51466000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:51456400-51460800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:51458000-51474800	Weak transcription	K562	blood
34	chr3:51458200-51466000	Weak transcription	Fetal Kidney	kidney
35	chr3:51458200-51466000	Weak transcription	NHEK	skin
36	chr3:51458200-51466200	Weak transcription	Colonic Mucosa	Colon
37	chr3:51458200-51474400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:51458200-51474600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:51458200-51475200	Weak transcription	NHLF	lung
40	chr3:51458200-51475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:51458200-51477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:51458200-51478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:51458200-51489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
45	chr3:51458400-51462400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:51458400-51463400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:51458400-51464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:51458400-51464400	Weak transcription	Lung	lung
49	chr3:51458400-51464400	Weak transcription	Osteobl	bone
50	chr3:51458400-51464600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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