Variant report

Variant	rs1861248
Chromosome Location	chr2:40098519-40098520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10188106	0.91[ASN][1000 genomes]
rs11692413	0.98[ASN][1000 genomes]
rs11695763	0.95[ASN][1000 genomes]
rs12475386	1.00[ASN][1000 genomes]
rs13424439	0.99[ASN][1000 genomes]
rs1541564	0.82[ASN][1000 genomes]
rs17024612	1.00[YRI][hapmap]
rs17480505	1.00[ASN][1000 genomes]
rs2080296	0.85[ASN][1000 genomes]
rs2192703	0.98[ASN][1000 genomes]
rs2373702	0.85[ASN][1000 genomes]
rs55768815	0.96[ASN][1000 genomes]
rs60399093	0.97[ASN][1000 genomes]
rs62137179	0.95[ASN][1000 genomes]
rs62137180	0.95[ASN][1000 genomes]
rs62137182	0.95[ASN][1000 genomes]
rs62137183	0.97[ASN][1000 genomes]
rs62137185	0.97[ASN][1000 genomes]
rs62137188	0.91[ASN][1000 genomes]
rs62137214	0.90[ASN][1000 genomes]
rs6732387	0.85[ASN][1000 genomes]
rs7556977	0.96[ASN][1000 genomes]
rs7562741	0.91[ASN][1000 genomes]
rs887994	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003593	chr2:40009597-40165666	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535651	chr2:40009597-40165666	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv873891	chr2:40046658-40173905	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv430947	chr2:40080723-40141649	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv581496	chr2:40082054-40123904	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1861248	PLEKHH2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40097000-40098800	Enhancers	Fetal Stomach	stomach
2	chr2:40097200-40098600	Enhancers	HSMMtube	muscle
3	chr2:40097200-40098800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:40097200-40098800	Enhancers	NHLF	lung
5	chr2:40097200-40099200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:40097200-40099200	Enhancers	HMEC	breast
7	chr2:40097200-40099200	Enhancers	NHEK	skin
8	chr2:40097400-40099200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:40097400-40099200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:40097400-40099200	Enhancers	NH-A	brain
11	chr2:40097400-40099200	Enhancers	NHDF-Ad	bronchial
12	chr2:40097400-40099200	Enhancers	Osteobl	bone
13	chr2:40097400-40099400	Enhancers	HSMM	muscle
14	chr2:40097600-40099000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:40097600-40099400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:40098000-40098600	Enhancers	Brain Anterior Caudate	brain
17	chr2:40098000-40098600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:40098000-40099200	Enhancers	Fetal Muscle Leg	muscle
19	chr2:40098200-40098800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:40098200-40098800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr2:40098200-40098800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:40098200-40098800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:40098400-40098600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:40098400-40098600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:40098400-40098800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:40098400-40098800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:40098400-40098800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:40098400-40098800	Enhancers	Dnd41	blood
29	chr2:40098400-40099000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:40098400-40099000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:40098400-40099000	Enhancers	Colon Smooth Muscle	Colon
32	chr2:40098400-40102200	Weak transcription	Stomach Smooth Muscle	stomach

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