Variant report

Variant	rs17220622
Chromosome Location	chr3:46579125-46579126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11705987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068099	0.80[CHB][hapmap];0.91[CHD][hapmap]
rs35167803	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35737208	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806702	1.00[MEX][hapmap]

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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876737	chr3:46569721-46595431	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17220622	LRRC2	cis	Liver	GTEx
rs17220622	TDGF1	cis	Muscle Skeletal	GTEx
rs17220622	TDGF1	cis	Adipose Subcutaneous	GTEx
rs17220622	SNRK	cis	cerebellum	SCAN
rs17220622	TDGF1	cis	Esophagus Muscularis	GTEx
rs17220622	ZNF33A	trans	cerebellum	SCAN
rs17220622	TDGF1	cis	parietal	SCAN
rs17220622	LRRC2	cis	multi-tissue	Pritchard
rs17220622	TDGF1	cis	lung	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46541000-46580200	Weak transcription	Fetal Heart	heart
2	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
3	chr3:46549200-46585400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:46556400-46591000	Weak transcription	Psoas Muscle	Psoas
5	chr3:46558400-46591000	Weak transcription	Gastric	stomach
6	chr3:46559000-46580000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:46559800-46580400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:46567200-46586000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:46569000-46584200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:46569600-46580200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:46571000-46583800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:46571600-46587000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:46577400-46579200	Enhancers	Dnd41	blood
14	chr3:46577400-46580600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:46577400-46581600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:46577600-46580400	Enhancers	Fetal Thymus	thymus
17	chr3:46577600-46580600	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:46577600-46581600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:46577800-46579200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:46577800-46579600	Enhancers	HSMM	muscle
21	chr3:46577800-46580600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:46578000-46579200	Enhancers	GM12878-XiMat	blood
23	chr3:46578000-46579400	Enhancers	Primary T cells from cord blood	blood
24	chr3:46578000-46580000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr3:46578000-46580400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:46578000-46580400	Enhancers	Thymus	Thymus
27	chr3:46578200-46580000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:46578200-46580200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:46578400-46579200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr3:46578400-46579200	Enhancers	Osteobl	bone
31	chr3:46578400-46580000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:46578400-46580600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:46578400-46580600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr3:46578400-46581000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:46578400-46581600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:46578400-46599200	Weak transcription	HSMMtube	muscle
37	chr3:46578600-46579400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:46578600-46579600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:46578600-46579600	Enhancers	Spleen	Spleen
40	chr3:46578600-46580000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:46578600-46580000	Enhancers	Primary B cells from cord blood	blood
42	chr3:46578600-46580000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:46578600-46580200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:46578600-46580200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:46578600-46580200	Weak transcription	K562	blood
46	chr3:46578800-46579800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:46578800-46580200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:46578800-46580200	Enhancers	Liver	Liver
49	chr3:46578800-46580400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:46578800-46581200	Weak transcription	Right Ventricle	heart

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