Variant report

Variant	rs9315458
Chromosome Location	chr13:37544226-37544227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:37544186-37544231	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ALG5	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12865199	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1924419	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1924420	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1924422	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1937761	0.87[EUR][1000 genomes]
rs2147169	0.88[EUR][1000 genomes]
rs2181787	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2186157	0.87[EUR][1000 genomes]
rs2323165	0.88[EUR][1000 genomes]
rs4291799	0.88[EUR][1000 genomes]
rs483304	0.83[AMR][1000 genomes]
rs4941854	0.86[EUR][1000 genomes]
rs4941855	0.86[EUR][1000 genomes]
rs4941856	0.85[EUR][1000 genomes]
rs568992	0.87[AMR][1000 genomes]
rs647421	0.83[AMR][1000 genomes]
rs6563507	0.88[EUR][1000 genomes]
rs71432622	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7317750	0.87[EUR][1000 genomes]
rs7321129	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7329314	0.87[EUR][1000 genomes]
rs7334233	0.88[EUR][1000 genomes]
rs7338929	0.85[EUR][1000 genomes]
rs7982674	0.88[EUR][1000 genomes]
rs7983986	0.87[EUR][1000 genomes]
rs7984730	0.83[EUR][1000 genomes]
rs7989205	0.86[EUR][1000 genomes]
rs7991057	0.87[EUR][1000 genomes]
rs7991181	0.87[EUR][1000 genomes]
rs8000534	0.80[AMR][1000 genomes]
rs9315459	0.88[EUR][1000 genomes]
rs9531998	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9532001	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9532002	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9532004	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9532005	0.88[EUR][1000 genomes]
rs9547707	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9547712	0.87[EUR][1000 genomes]
rs9547715	0.87[EUR][1000 genomes]
rs9547717	0.92[EUR][1000 genomes]
rs9547718	0.87[EUR][1000 genomes]
rs9576153	0.88[EUR][1000 genomes]
rs9576154	0.88[EUR][1000 genomes]
rs9594181	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9603121	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9315458	SUPT20H	cis	Whole Blood	GTEx
rs9315458	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
3	chr13:37522600-37548800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:37522800-37547000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:37523000-37545600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr13:37523200-37558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
8	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:37524800-37546400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:37525000-37560800	Weak transcription	Fetal Heart	heart
11	chr13:37525600-37544800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:37526600-37556200	Weak transcription	Brain Angular Gyrus	brain
13	chr13:37526800-37559400	Weak transcription	Hela-S3	cervix
14	chr13:37528800-37546200	Strong transcription	Fetal Thymus	thymus
15	chr13:37529400-37546800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:37529400-37558200	Weak transcription	Gastric	stomach
17	chr13:37529600-37555600	Weak transcription	Stomach Mucosa	stomach
18	chr13:37530600-37545600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr13:37531800-37570000	Strong transcription	Dnd41	blood
20	chr13:37532000-37546000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr13:37532400-37545800	Strong transcription	Liver	Liver
22	chr13:37532400-37546200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr13:37533000-37546400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:37533400-37545400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:37533400-37546200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:37534000-37545600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr13:37534800-37546000	Strong transcription	Placenta	Placenta
28	chr13:37535000-37545800	Strong transcription	Adipose Nuclei	Adipose
29	chr13:37535200-37553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr13:37535400-37549600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr13:37536000-37545400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr13:37536400-37546400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr13:37537400-37546200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr13:37539000-37544400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:37539000-37558400	Weak transcription	Colonic Mucosa	Colon
36	chr13:37539000-37561000	Weak transcription	Aorta	Aorta
37	chr13:37539200-37545200	Weak transcription	Lung	lung
38	chr13:37539200-37558000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr13:37539400-37545400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:37539400-37561000	Weak transcription	Right Ventricle	heart
41	chr13:37539400-37562400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr13:37539600-37549000	Weak transcription	Ovary	ovary
43	chr13:37539600-37558200	Weak transcription	Brain Germinal Matrix	brain
44	chr13:37539600-37562400	Weak transcription	Fetal Brain Male	brain
45	chr13:37539800-37545400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr13:37539800-37557600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr13:37540200-37544400	Weak transcription	Thymus	Thymus
48	chr13:37540200-37544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr13:37540200-37544800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr13:37540200-37548000	Weak transcription	Stomach Smooth Muscle	stomach

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