Variant report

Variant	rs936580
Chromosome Location	chr15:40924578-40924579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10400825	0.87[EUR][1000 genomes]
rs10467972	0.80[EUR][1000 genomes]
rs10744948	0.85[EUR][1000 genomes]
rs11070284	0.95[EUR][1000 genomes]
rs11561564	0.81[EUR][1000 genomes]
rs11638204	0.84[EUR][1000 genomes]
rs11854763	0.95[EUR][1000 genomes]
rs12438955	0.95[EUR][1000 genomes]
rs12440468	0.80[EUR][1000 genomes]
rs12592882	0.82[EUR][1000 genomes]
rs12708401	0.95[EUR][1000 genomes]
rs12899600	0.88[EUR][1000 genomes]
rs12906095	0.81[EUR][1000 genomes]
rs12911738	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12912058	0.95[EUR][1000 genomes]
rs12912339	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12915109	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916082	0.86[EUR][1000 genomes]
rs1901775	0.82[EUR][1000 genomes]
rs2278888	0.80[EUR][1000 genomes]
rs2304580	0.82[EUR][1000 genomes]
rs2412541	0.95[EUR][1000 genomes]
rs2619681	0.85[EUR][1000 genomes]
rs3092978	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34285050	0.85[EUR][1000 genomes]
rs4306472	0.91[EUR][1000 genomes]
rs4417527	0.85[EUR][1000 genomes]
rs4420508	0.95[EUR][1000 genomes]
rs4439732	0.80[EUR][1000 genomes]
rs45457497	0.82[EUR][1000 genomes]
rs4924484	0.96[EUR][1000 genomes]
rs4924487	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924488	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924491	0.90[EUR][1000 genomes]
rs4924500	0.85[EUR][1000 genomes]
rs55640412	0.80[EUR][1000 genomes]
rs6492957	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492958	0.89[EUR][1000 genomes]
rs66885559	0.81[EUR][1000 genomes]
rs7161938	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7161968	0.87[EUR][1000 genomes]
rs7162509	0.81[EUR][1000 genomes]
rs7164289	0.88[EUR][1000 genomes]
rs7167417	0.95[EUR][1000 genomes]
rs7167768	0.82[EUR][1000 genomes]
rs7168873	0.90[EUR][1000 genomes]
rs7171260	0.95[EUR][1000 genomes]
rs7171945	0.80[EUR][1000 genomes]
rs7172947	0.87[EUR][1000 genomes]
rs7176974	0.95[EUR][1000 genomes]
rs7177192	0.95[EUR][1000 genomes]
rs7178486	0.95[EUR][1000 genomes]
rs8028999	0.80[EUR][1000 genomes]
rs8031057	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8035775	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8037804	0.95[EUR][1000 genomes]
rs8040502	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8041443	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9806221	0.94[EUR][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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs936580	RMDN3	cis	Heart Left Ventricle	GTEx
rs936580	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
2	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:40890800-40925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:40900000-40943600	Weak transcription	NH-A	brain
12	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
13	chr15:40903600-40927800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
17	chr15:40904800-40927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:40906400-40930200	Strong transcription	Dnd41	blood
19	chr15:40910200-40925200	Weak transcription	Placenta	Placenta
20	chr15:40911400-40930600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
22	chr15:40912600-40941400	Weak transcription	HepG2	liver
23	chr15:40913800-40986000	Weak transcription	A549	lung
24	chr15:40914400-40960000	Weak transcription	NHLF	lung
25	chr15:40914800-40924600	Weak transcription	HMEC	breast
26	chr15:40914800-40933200	Weak transcription	NHDF-Ad	bronchial
27	chr15:40914800-40942600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:40915600-40927200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:40915600-40937000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:40915600-40937000	Weak transcription	HUVEC	blood vessel
31	chr15:40916200-40927800	Weak transcription	HSMM	muscle
32	chr15:40918000-40924600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:40918600-40929200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:40918800-40933400	Strong transcription	Thymus	Thymus
35	chr15:40919200-40935200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
38	chr15:40919800-40938400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:40920200-40933400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:40920400-40925000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:40920600-40925400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:40921800-40929000	Strong transcription	Fetal Stomach	stomach
44	chr15:40922200-40925000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr15:40922200-40928600	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:40922200-40930000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:40922400-40938400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:40922600-40926600	Strong transcription	Fetal Intestine Small	intestine
49	chr15:40922600-40927000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:40922600-40928600	Strong transcription	Fetal Muscle Trunk	muscle

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