Variant report

Variant	rs3781196
Chromosome Location	chr10:90042154-90042155
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10509540	0.84[ASN][1000 genomes]
rs12415812	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12416116	0.89[ASN][1000 genomes]
rs166976	0.84[ASN][1000 genomes]
rs17110523	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2018705	0.88[ASN][1000 genomes]
rs286487	0.86[ASN][1000 genomes]
rs3781197	0.87[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45585838	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558443	0.90[EUR][1000 genomes]
rs60888743	0.86[ASN][1000 genomes]
rs7068821	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7094781	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737391	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7922058	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9665166	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467414	chr10:90006507-90042154	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3781196	LIPJ	cis	cerebellum	SCAN
rs3781196	CH25H	cis	cerebellum	SCAN
rs3781196	PCGF5	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90032800-90042400	Weak transcription	Right Atrium	heart
2	chr10:90037800-90043200	Enhancers	Dnd41	blood
3	chr10:90038600-90042800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr10:90038800-90043000	Enhancers	Fetal Thymus	thymus
5	chr10:90039000-90043000	Enhancers	Primary hematopoietic stem cells	blood
6	chr10:90039200-90042800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr10:90039800-90042600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr10:90039800-90042800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr10:90039800-90043000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:90039800-90043000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:90040400-90042200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr10:90040600-90042800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:90040600-90042800	Enhancers	HMEC	breast
14	chr10:90041000-90042200	Enhancers	A549	lung
15	chr10:90041000-90042800	Enhancers	Thymus	Thymus
16	chr10:90041000-90042800	Enhancers	Hela-S3	cervix
17	chr10:90041200-90042600	Enhancers	Primary B cells from cord blood	blood
18	chr10:90041200-90042800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:90041200-90043200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:90041400-90042200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr10:90041400-90042200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr10:90041400-90042400	Flanking Active TSS	NH-A	brain
23	chr10:90041400-90042600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr10:90041400-90042800	Flanking Active TSS	Osteobl	bone
25	chr10:90041400-90043000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:90041600-90042200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:90041600-90042400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:90041600-90042400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr10:90041600-90042600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:90041600-90042800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:90041600-90042800	Enhancers	Primary B cells from peripheral blood	blood
32	chr10:90041600-90042800	Enhancers	Primary T cells from cord blood	blood
33	chr10:90041600-90042800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:90041600-90042800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:90041600-90042800	Enhancers	HSMM	muscle
36	chr10:90041600-90042800	Flanking Active TSS	NHDF-Ad	bronchial
37	chr10:90041600-90042800	Enhancers	NHEK	skin
38	chr10:90041600-90043000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:90041600-90043000	Enhancers	Fetal Lung	lung
40	chr10:90041800-90042200	Enhancers	GM12878-XiMat	blood
41	chr10:90041800-90042400	Enhancers	Colon Smooth Muscle	Colon
42	chr10:90041800-90042400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr10:90041800-90042400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr10:90041800-90042600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr10:90041800-90042600	Flanking Active TSS	HSMMtube	muscle
46	chr10:90041800-90042800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr10:90041800-90042800	Flanking Active TSS	NHLF	lung
48	chr10:90042000-90042200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr10:90042000-90042400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr10:90042000-90042400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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