Variant report

Variant	rs1836850
Chromosome Location	chr15:40120504-40120505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1027232	0.88[JPT][hapmap]
rs11070235	0.85[ASN][1000 genomes]
rs1166729	0.87[ASN][1000 genomes]
rs11854663	0.86[ASN][1000 genomes]
rs11855441	0.86[ASN][1000 genomes]
rs11858909	0.85[LWK][hapmap];0.82[YRI][hapmap]
rs12438821	0.97[ASN][1000 genomes]
rs12442442	0.86[ASN][1000 genomes]
rs1436274	0.85[ASN][1000 genomes]
rs1865754	0.96[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs2029584	0.83[MEX][hapmap]
rs275720	0.80[EUR][1000 genomes]
rs275754	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28565083	0.97[ASN][1000 genomes]
rs35194933	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784392	0.96[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs4923842	0.86[ASN][1000 genomes]
rs4923843	0.86[ASN][1000 genomes]
rs4924390	0.83[MEX][hapmap]
rs4924393	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4924394	0.86[ASN][1000 genomes]
rs62002492	0.85[ASN][1000 genomes]
rs62002493	0.85[ASN][1000 genomes]
rs7179742	0.83[MEX][hapmap]
rs7180846	0.83[MEX][hapmap]
rs7181712	0.86[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	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
2	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
3	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1836850	C15orf54	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40103000-40121400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:40110400-40129800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:40111600-40123400	Weak transcription	Aorta	Aorta
4	chr15:40112600-40120600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:40112600-40121400	Weak transcription	Right Atrium	heart
6	chr15:40114400-40121400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:40116000-40122600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:40116200-40122600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:40116800-40125600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:40117000-40121200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:40118200-40121800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:40119600-40120800	Enhancers	Fetal Brain Female	brain
13	chr15:40119800-40121600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:40120000-40121400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr15:40120000-40123200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:40120200-40121200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:40120200-40121400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:40120200-40121600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:40120200-40123600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:40120200-40123600	Enhancers	NHLF	lung
21	chr15:40120400-40120800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr15:40120400-40120800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:40120400-40120800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:40120400-40120800	Enhancers	Brain Cingulate Gyrus	brain
25	chr15:40120400-40120800	Enhancers	Brain Germinal Matrix	brain
26	chr15:40120400-40120800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr15:40120400-40120800	Enhancers	Esophagus	oesophagus
28	chr15:40120400-40120800	Enhancers	Fetal Muscle Leg	muscle
29	chr15:40120400-40120800	Enhancers	Lung	lung
30	chr15:40120400-40120800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:40120400-40120800	Enhancers	HSMMtube	muscle
32	chr15:40120400-40121000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:40120400-40121000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:40120400-40121000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:40120400-40121000	Enhancers	Brain Anterior Caudate	brain
36	chr15:40120400-40121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:40120400-40121400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:40120400-40121600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:40120400-40121600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr15:40120400-40121600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr15:40120400-40121600	Genic enhancers	HSMM	muscle
42	chr15:40120400-40121600	Enhancers	NH-A	brain
43	chr15:40120400-40121600	Enhancers	NHDF-Ad	bronchial
44	chr15:40120400-40121800	Enhancers	Osteobl	bone
45	chr15:40120400-40122000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr15:40120400-40122000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:40120400-40122000	Enhancers	HUVEC	blood vessel
48	chr15:40120400-40123800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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