Variant report

Variant	rs12594415
Chromosome Location	chr15:83527562-83527563
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12442119	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1256424	0.85[AFR][1000 genomes]
rs3784376	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784377	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs899746	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12594415	C15orf40	cis	brain	BrainEAC
rs12594415	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs12594415	BTBD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:83519600-83529600	Weak transcription	Brain Substantia Nigra	brain
11	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:83520000-83543600	Weak transcription	HSMM	muscle
13	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
16	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:83521800-83529400	Weak transcription	Primary B cells from cord blood	blood
18	chr15:83522400-83543400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:83522600-83529000	Weak transcription	Fetal Kidney	kidney
20	chr15:83522600-83542200	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:83523400-83540000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:83523400-83540800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:83523600-83541400	Weak transcription	Fetal Stomach	stomach
24	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
25	chr15:83523800-83535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:83524600-83527800	Weak transcription	Spleen	Spleen
27	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
28	chr15:83524800-83528800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:83524800-83534400	Weak transcription	Adipose Nuclei	Adipose
30	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:83525600-83528000	Strong transcription	Gastric	stomach
32	chr15:83525800-83529800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:83526000-83541800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:83527000-83528000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:83527200-83528000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:83527200-83539600	Weak transcription	HSMMtube	muscle
37	chr15:83527400-83528000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:83527400-83528000	Genic enhancers	Pancreas	Pancrea
39	chr15:83527400-83528600	Strong transcription	Liver	Liver

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