Variant report

Variant	rs4924389
Chromosome Location	chr15:40063967-40063968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1021410	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1021411	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1166716	1.00[CEU][hapmap]
rs1166718	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1166722	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1166723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592687	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565559	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1565561	0.88[CEU][hapmap]
rs1688087	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1844863	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1906163	1.00[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1906164	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2029584	0.85[CEU][hapmap]
rs2576929	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2576933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2638009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28450006	0.83[EUR][1000 genomes]
rs34320375	0.82[EUR][1000 genomes]
rs34943556	0.93[ASN][1000 genomes]
rs4115216	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4924385	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924391	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592172	0.95[ASN][1000 genomes]
rs594863	0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs606927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs62004808	0.81[EUR][1000 genomes]
rs620407	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6492914	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6492915	0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6492919	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs66496275	0.93[ASN][1000 genomes]
rs670748	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7165244	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7179417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7179742	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7179838	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7180846	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs8031241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033485	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8033957	0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4924389	RPAP1	cis	parietal	SCAN
rs4924389	C15orf54	cis	cerebellum	SCAN
rs4924389	GJD2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40053400-40069400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40054400-40069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:40059400-40074400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:40063000-40064200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr15:40063000-40064200	Enhancers	Small Intestine	intestine
6	chr15:40063000-40064400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:40063000-40064400	Enhancers	Fetal Stomach	stomach
8	chr15:40063000-40064600	Enhancers	Fetal Muscle Leg	muscle
9	chr15:40063200-40064400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:40063200-40064400	Enhancers	Colon Smooth Muscle	Colon
11	chr15:40063200-40064400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr15:40063200-40066600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:40063400-40064000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:40063400-40064000	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr15:40063400-40064200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:40063400-40064200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:40063400-40064200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:40063400-40064200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:40063400-40064200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:40063400-40064200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:40063400-40064200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:40063400-40064200	Flanking Active TSS	HSMMtube	muscle
23	chr15:40063400-40064400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:40063400-40064400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:40063400-40064400	Flanking Active TSS	Osteobl	bone
26	chr15:40063600-40064000	Flanking Active TSS	Brain Substantia Nigra	brain
27	chr15:40063600-40064000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr15:40063600-40064000	Active TSS	Stomach Smooth Muscle	stomach
29	chr15:40063600-40064000	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr15:40063600-40064000	Flanking Active TSS	NH-A	brain
31	chr15:40063600-40064000	Active TSS	NHDF-Ad	bronchial
32	chr15:40063600-40064200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr15:40063600-40064200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:40063600-40064400	Enhancers	Lung	lung
35	chr15:40063800-40064000	Active TSS	Brain Anterior Caudate	brain
36	chr15:40063800-40064000	Enhancers	Rectal Smooth Muscle	rectum
37	chr15:40063800-40064000	Active TSS	HepG2	liver
38	chr15:40063800-40064200	Flanking Active TSS	HSMM	muscle
39	chr15:40063800-40064200	Flanking Active TSS	NHLF	lung
40	chr15:40063800-40064400	Enhancers	Adipose Nuclei	Adipose
41	chr15:40063800-40064600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:40063800-40065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:40063800-40066600	Weak transcription	GM12878-XiMat	blood
44	chr15:40063800-40067800	Weak transcription	Esophagus	oesophagus
45	chr15:40063800-40068800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:40063800-40068800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr15:40063800-40069000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:40063800-40074000	Weak transcription	Brain Angular Gyrus	brain

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