Variant report

Variant	rs2255942
Chromosome Location	chr3:100701849-100701850
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1463187	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1823361	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1839296	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2595886	0.88[ASN][1000 genomes]
rs2595903	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2713753	0.88[ASN][1000 genomes]
rs2713777	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv525082	chr3:100699827-100703124	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2255942	IMPG2	cis	cerebellum	SCAN
rs2255942	NIT2	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100692600-100711200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:100696200-100702200	Enhancers	Fetal Stomach	stomach
3	chr3:100700000-100702200	Enhancers	Fetal Muscle Leg	muscle
4	chr3:100700400-100702000	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr3:100700400-100711200	Weak transcription	Esophagus	oesophagus
6	chr3:100701200-100702200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:100701400-100702000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:100701400-100702000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:100701400-100702000	Flanking Active TSS	Colon Smooth Muscle	Colon
10	chr3:100701400-100702000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:100701400-100702000	Enhancers	Fetal Heart	heart
12	chr3:100701400-100702000	Flanking Active TSS	Fetal Lung	lung
13	chr3:100701400-100702000	Flanking Active TSS	Ovary	ovary
14	chr3:100701400-100702000	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr3:100701400-100702000	Flanking Active TSS	Osteobl	bone
16	chr3:100701600-100702000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:100701600-100702000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:100701600-100702000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr3:100701600-100702000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:100701600-100702000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:100701600-100702000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:100701600-100702000	Enhancers	Adipose Nuclei	Adipose
23	chr3:100701600-100702000	Active TSS	Brain Hippocampus Middle	brain
24	chr3:100701600-100702000	Enhancers	Gastric	stomach
25	chr3:100701600-100702000	Enhancers	Left Ventricle	heart
26	chr3:100701600-100702000	Enhancers	Psoas Muscle	Psoas
27	chr3:100701600-100702000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:100701600-100702000	Active TSS	NHLF	lung
29	chr3:100701600-100702200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:100701800-100702000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:100701800-100702000	Enhancers	Fetal Muscle Trunk	muscle
32	chr3:100701800-100702000	Flanking Active TSS	HSMM	muscle
33	chr3:100701800-100702000	Flanking Active TSS	HUVEC	blood vessel
34	chr3:100701800-100702000	Flanking Active TSS	NHDF-Ad	bronchial
35	chr3:100701800-100702200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:100701800-100702200	Enhancers	HSMMtube	muscle
37	chr3:100701800-100711000	Weak transcription	Aorta	Aorta

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