Variant report

Variant	rs1924420
Chromosome Location	chr13:37530840-37530841
allele	A/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]
rs12865199	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1924419	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1924421	0.83[EUR][1000 genomes]
rs1924422	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1937761	0.96[EUR][1000 genomes]
rs2147169	0.97[EUR][1000 genomes]
rs2181787	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2181788	0.83[EUR][1000 genomes]
rs2186157	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2323165	0.97[EUR][1000 genomes]
rs4291799	0.97[EUR][1000 genomes]
rs4624036	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs483304	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4941854	0.95[EUR][1000 genomes]
rs4941855	0.95[EUR][1000 genomes]
rs4941856	0.94[EUR][1000 genomes]
rs568992	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs647421	0.91[AMR][1000 genomes]
rs6563506	0.83[EUR][1000 genomes]
rs6563507	0.97[EUR][1000 genomes]
rs71432622	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7317750	0.96[EUR][1000 genomes]
rs7321129	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7329314	0.96[EUR][1000 genomes]
rs7334233	0.97[EUR][1000 genomes]
rs7338929	0.94[EUR][1000 genomes]
rs7982674	0.97[EUR][1000 genomes]
rs7983986	0.96[EUR][1000 genomes]
rs7984730	0.92[EUR][1000 genomes]
rs7989205	0.95[EUR][1000 genomes]
rs7991057	0.96[EUR][1000 genomes]
rs7991181	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9315458	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9315459	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9531998	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9532001	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9532002	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9532004	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9532005	0.97[EUR][1000 genomes]
rs9547705	0.80[AMR][1000 genomes]
rs9547707	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9547712	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9547715	0.96[EUR][1000 genomes]
rs9547717	0.94[EUR][1000 genomes]
rs9547718	0.96[EUR][1000 genomes]
rs9576148	0.82[AMR][1000 genomes]
rs9576153	0.97[EUR][1000 genomes]
rs9576154	0.97[EUR][1000 genomes]
rs9594181	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9603121	0.98[AMR][1000 genomes];0.96[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
rs1924420	SUPT20H	cis	Whole Blood	GTEx
rs1924420	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:37520400-37538000	Weak transcription	Colonic Mucosa	Colon
5	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
6	chr13:37520800-37538000	Weak transcription	HepG2	liver
7	chr13:37521000-37536600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:37521200-37538200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:37521400-37531000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr13:37521400-37531000	Strong transcription	Liver	Liver
11	chr13:37521400-37532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:37521400-37537800	Weak transcription	NHLF	lung
13	chr13:37521400-37538000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:37521400-37538400	Weak transcription	Aorta	Aorta
15	chr13:37521400-37542800	Weak transcription	A549	lung
16	chr13:37521600-37532600	Strong transcription	Primary T cells from cord blood	blood
17	chr13:37521600-37534800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:37521600-37535200	Weak transcription	NHEK	skin
19	chr13:37521600-37537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr13:37521600-37538000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr13:37521600-37538000	Weak transcription	Brain Hippocampus Middle	brain
22	chr13:37521600-37538200	Weak transcription	HSMMtube	muscle
23	chr13:37521800-37539200	Weak transcription	K562	blood
24	chr13:37522000-37531200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr13:37522000-37538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:37522000-37538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:37522400-37531000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr13:37522600-37541000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:37522600-37548800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:37522800-37547000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:37523000-37531000	Strong transcription	Dnd41	blood
32	chr13:37523000-37531400	Weak transcription	Fetal Intestine Small	intestine
33	chr13:37523000-37532400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:37523000-37532800	Strong transcription	Fetal Intestine Large	intestine
35	chr13:37523000-37538400	Weak transcription	Lung	lung
36	chr13:37523000-37545600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr13:37523200-37558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:37523400-37538000	Weak transcription	Brain Substantia Nigra	brain
39	chr13:37523400-37538000	Weak transcription	Esophagus	oesophagus
40	chr13:37523600-37533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:37523600-37536600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:37523800-37536800	Weak transcription	Brain Germinal Matrix	brain
43	chr13:37523800-37538000	Weak transcription	Brain Anterior Caudate	brain
44	chr13:37524000-37531400	Weak transcription	Spleen	Spleen
45	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
46	chr13:37524600-37538400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr13:37524800-37546400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:37525000-37560800	Weak transcription	Fetal Heart	heart
50	chr13:37525600-37535000	Weak transcription	NHDF-Ad	bronchial

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