Variant report

Variant	rs1348109
Chromosome Location	chr3:16949514-16949515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10865746	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11926952	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12233492	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12487288	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs12497667	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13058764	0.83[JPT][hapmap]
rs13080108	0.90[JPT][hapmap]
rs1441035	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1441039	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17272796	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1806556	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1837698	0.96[ASN][1000 genomes]
rs2014490	0.84[TSI][hapmap]
rs34149515	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924971	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4353792	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4461404	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs4472039	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4535211	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs4602367	0.85[JPT][hapmap]
rs4618210	0.80[JPT][hapmap]
rs4685400	0.93[ASN][1000 genomes]
rs4685404	0.96[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4685409	0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4685418	0.80[CEU][hapmap]
rs4685427	0.80[JPT][hapmap]
rs6442660	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6762816	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6780191	0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6781611	0.81[ASN][1000 genomes]
rs6783752	0.91[ASN][1000 genomes]
rs6809087	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs7610811	0.82[CHB][hapmap]
rs7611127	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs7612044	0.84[JPT][hapmap]
rs7617672	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7629171	0.80[ASN][1000 genomes]
rs7629676	0.91[ASN][1000 genomes]
rs7653027	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs9810017	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9830460	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9841259	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9854760	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9862613	0.88[JPT][hapmap]
rs9879150	0.80[JPT][hapmap]
rs9880307	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1348109	TMEM43	cis	cerebellum	SCAN
rs1348109	C3orf20	cis	cerebellum	SCAN
rs1348109	CHCHD4	cis	parietal	SCAN
rs1348109	SGOL1	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16931200-16952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:16936200-16949600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:16939400-16950000	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:16940800-16950000	Weak transcription	Esophagus	oesophagus
5	chr3:16940800-16954200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:16940800-16962200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:16941800-16959400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:16942800-16952000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:16943200-16952200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:16943400-16950400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:16943600-16950000	Weak transcription	Placenta	Placenta
12	chr3:16943600-16952600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:16943800-16950200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:16943800-16954200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:16945600-16951800	Enhancers	Fetal Heart	heart
16	chr3:16946200-16959000	Weak transcription	Aorta	Aorta
17	chr3:16946400-16951200	Enhancers	Primary B cells from cord blood	blood
18	chr3:16946600-16950000	Weak transcription	Fetal Brain Female	brain
19	chr3:16946600-16950000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr3:16946600-16950200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:16946800-16950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:16947200-16951000	Enhancers	Primary hematopoietic stem cells	blood
23	chr3:16947400-16950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:16947400-16951400	Weak transcription	Fetal Brain Male	brain
25	chr3:16947400-16951400	Weak transcription	Right Ventricle	heart
26	chr3:16947600-16950200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:16947800-16950200	Enhancers	NH-A	brain
28	chr3:16947800-16951400	Weak transcription	Brain Germinal Matrix	brain
29	chr3:16948000-16950000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:16948000-16952400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr3:16948200-16949800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:16948200-16949800	Enhancers	Osteobl	bone
33	chr3:16948400-16950200	Enhancers	NHLF	lung
34	chr3:16948600-16950000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:16948600-16950200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:16948800-16949800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:16948800-16950000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:16948800-16950200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:16949000-16951200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:16949000-16951400	Weak transcription	Brain Anterior Caudate	brain
41	chr3:16949000-16951600	Enhancers	Primary T cells from cord blood	blood
42	chr3:16949000-16951600	Weak transcription	Brain Substantia Nigra	brain
43	chr3:16949000-16952200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:16949000-16952400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:16949000-16952600	Weak transcription	Fetal Stomach	stomach
46	chr3:16949000-16953200	Weak transcription	NHDF-Ad	bronchial
47	chr3:16949000-16965400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:16949200-16949800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:16949200-16950000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:16949200-16950000	Flanking Active TSS	HUVEC	blood vessel

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