Variant report

Variant	rs1780747
Chromosome Location	chr1:79181416-79181417
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11577395	0.95[JPT][hapmap]
rs11804167	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12409167	0.81[ASN][1000 genomes]
rs1547181	0.82[ASN][1000 genomes]
rs2148689	0.83[EUR][1000 genomes]
rs3766325	0.88[ASW][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap]
rs56216300	0.82[ASN][1000 genomes]
rs6424781	0.82[ASN][1000 genomes]
rs6669498	0.95[JPT][hapmap]
rs6695058	0.82[ASN][1000 genomes]
rs7514391	0.95[JPT][hapmap];0.85[TSI][hapmap]
rs7517942	0.82[ASN][1000 genomes]
rs7523042	0.82[ASN][1000 genomes]
rs7526598	0.82[ASN][1000 genomes]
rs7526782	0.81[ASN][1000 genomes]
rs7526927	0.82[ASN][1000 genomes]
rs7533325	0.82[ASN][1000 genomes]
rs7543088	0.82[ASN][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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv871588	chr1:79164901-79214489	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1780747	IFI44	cis	parietal	SCAN
rs1780747	ZZZ3	cis	cerebellum	SCAN
rs1780747	IFI44	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79178400-79184800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:79178400-79185000	Enhancers	Osteobl	bone
3	chr1:79179800-79183400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:79180000-79184600	Enhancers	NHDF-Ad	bronchial
5	chr1:79180200-79182400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:79180400-79182000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:79180600-79181800	Enhancers	NHLF	lung
8	chr1:79180600-79182000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:79180600-79184800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:79180800-79181800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:79180800-79181800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:79180800-79182800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:79180800-79182800	Enhancers	HSMMtube	muscle
14	chr1:79181000-79181600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:79181000-79181800	Enhancers	HSMM	muscle
16	chr1:79181000-79182000	Enhancers	NH-A	brain
17	chr1:79181200-79181600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:79181400-79182000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:79181400-79182400	Weak transcription	HUVEC	blood vessel
20	chr1:79181400-79182600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:79181400-79183600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:79181400-79184200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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