Variant report

Variant	rs9531998
Chromosome Location	chr13:37525567-37525568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1199963	0.82[AFR][1000 genomes]
rs12865199	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1924419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1924420	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1924421	0.84[EUR][1000 genomes]
rs1924422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1937761	0.97[EUR][1000 genomes]
rs2147169	0.99[EUR][1000 genomes]
rs2181787	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181788	0.84[EUR][1000 genomes]
rs2186157	0.97[EUR][1000 genomes]
rs2323165	0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4291799	0.99[EUR][1000 genomes]
rs4624036	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs483304	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4941854	0.96[EUR][1000 genomes]
rs4941855	0.96[EUR][1000 genomes]
rs4941856	0.95[EUR][1000 genomes]
rs568992	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs647421	0.93[AMR][1000 genomes]
rs6563506	0.84[EUR][1000 genomes]
rs6563507	0.99[EUR][1000 genomes]
rs71432622	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7317750	0.97[EUR][1000 genomes]
rs7321129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7329314	0.97[EUR][1000 genomes]
rs7334233	0.99[EUR][1000 genomes]
rs7338929	0.95[EUR][1000 genomes]
rs7982674	0.99[EUR][1000 genomes]
rs7983986	0.97[EUR][1000 genomes]
rs7984730	0.94[EUR][1000 genomes]
rs7989205	0.96[EUR][1000 genomes]
rs7991057	0.97[EUR][1000 genomes]
rs7991181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9315458	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9315459	0.99[EUR][1000 genomes]
rs9532001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532002	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532004	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9532005	0.99[EUR][1000 genomes]
rs9547705	0.82[AMR][1000 genomes]
rs9547707	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9547712	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9547715	0.97[EUR][1000 genomes]
rs9547717	0.95[EUR][1000 genomes]
rs9547718	0.97[EUR][1000 genomes]
rs9576153	0.99[EUR][1000 genomes]
rs9576154	0.99[EUR][1000 genomes]
rs9594181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9603121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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
rs9531998	FAM48A	Cis_1M	lymphoblastoid	RTeQTL
rs9531998	SUPT20H	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37515400-37533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:37517200-37538400	Weak transcription	Fetal Brain Male	brain
3	chr13:37517600-37529000	Weak transcription	Thymus	Thymus
4	chr13:37519400-37527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:37519400-37528800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:37520400-37538000	Weak transcription	Colonic Mucosa	Colon
8	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
9	chr13:37520800-37529000	Weak transcription	Gastric	stomach
10	chr13:37520800-37529400	Weak transcription	HMEC	breast
11	chr13:37520800-37538000	Weak transcription	HepG2	liver
12	chr13:37521000-37536600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr13:37521200-37538200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:37521400-37526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:37521400-37527800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:37521400-37528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:37521400-37528800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:37521400-37529200	Weak transcription	Fetal Kidney	kidney
19	chr13:37521400-37529400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:37521400-37531000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:37521400-37531000	Strong transcription	Liver	Liver
22	chr13:37521400-37532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:37521400-37537800	Weak transcription	NHLF	lung
24	chr13:37521400-37538000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:37521400-37538400	Weak transcription	Aorta	Aorta
26	chr13:37521400-37542800	Weak transcription	A549	lung
27	chr13:37521600-37526600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:37521600-37527400	Strong transcription	Adipose Nuclei	Adipose
29	chr13:37521600-37527800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:37521600-37532600	Strong transcription	Primary T cells from cord blood	blood
31	chr13:37521600-37534800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:37521600-37535200	Weak transcription	NHEK	skin
33	chr13:37521600-37537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr13:37521600-37538000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr13:37521600-37538000	Weak transcription	Brain Hippocampus Middle	brain
36	chr13:37521600-37538200	Weak transcription	HSMMtube	muscle
37	chr13:37521800-37539200	Weak transcription	K562	blood
38	chr13:37522000-37531200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr13:37522000-37538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:37522000-37538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr13:37522200-37526600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:37522200-37527200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:37522200-37527600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr13:37522400-37531000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:37522600-37525800	Strong transcription	Fetal Brain Female	brain
46	chr13:37522600-37526800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:37522600-37527400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr13:37522600-37527600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:37522600-37541000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:37522600-37548800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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