Variant report

Variant	rs62298302
Chromosome Location	chr4:47928716-47928717
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:47928329..47929479-chr4:48088621..48089783,3	K562	blood:
2	chr4:47914012..47917930-chr4:47928517..47931716,3	K562	blood:
3	chr4:47928537..47929256-chr4:48142747..48143293,3	K562	blood:

Variant related genes	Relation type
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10008818	0.86[ASN][1000 genomes]
rs1012844	0.86[ASN][1000 genomes]
rs10517201	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10938502	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10938509	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11722700	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737879	0.92[ASN][1000 genomes]
rs11933101	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11934632	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11937912	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11940319	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940441	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12501861	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501949	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505333	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506863	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12509420	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12509520	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510304	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512884	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512988	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513157	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1465885	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860663	0.80[ASN][1000 genomes]
rs17463534	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17573717	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1822029	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1965804	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992326	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165263	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2882949	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34449323	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4031458	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405986	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4435717	0.86[ASN][1000 genomes]
rs4475122	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4518214	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4695278	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4695280	0.80[ASN][1000 genomes]
rs4695317	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844485	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56084299	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56384707	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56686194	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56971681	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57159058	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60535228	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62298261	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62298266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62298267	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62298303	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62298344	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62299256	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62299257	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62299258	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62299259	0.86[ASN][1000 genomes]
rs62301160	0.90[ASN][1000 genomes]
rs62301163	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447585	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447591	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66901846	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816253	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6819172	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6820636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6833422	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6844066	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6845064	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848667	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654965	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690499	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699225	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62298302	NFXL1	cis	Whole Blood	GTEx
rs62298302	CORIN	cis	Whole Blood	GTEx
rs62298302	RP11-121C2.2	cis	Whole Blood	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47924800-47928800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:47924800-47928800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:47924800-47928800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:47925000-47928800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:47925000-47928800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:47925000-47928800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:47925000-47928800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:47925000-47928800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:47925000-47928800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:47925200-47928800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:47926000-47928800	Weak transcription	GM12878-XiMat	blood
12	chr4:47926200-47928800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:47928200-47928800	Enhancers	Fetal Intestine Large	intestine
14	chr4:47928200-47929200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:47928400-47928800	Active TSS	Brain Cingulate Gyrus	brain
16	chr4:47928400-47928800	Enhancers	NHEK	skin
17	chr4:47928400-47929000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr4:47928400-47929200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:47928600-47928800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:47928600-47928800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:47928600-47928800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:47928600-47928800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:47928600-47928800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:47928600-47928800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:47928600-47928800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr4:47928600-47928800	Enhancers	Primary T cells from cord blood	blood
27	chr4:47928600-47928800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr4:47928600-47928800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:47928600-47928800	Active TSS	Brain Anterior Caudate	brain
30	chr4:47928600-47928800	Enhancers	Brain Hippocampus Middle	brain
31	chr4:47928600-47928800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:47928600-47928800	Enhancers	Brain Substantia Nigra	brain
33	chr4:47928600-47928800	Enhancers	Colonic Mucosa	Colon
34	chr4:47928600-47928800	Enhancers	Duodenum Mucosa	Duodenum
35	chr4:47928600-47928800	Enhancers	Fetal Stomach	stomach
36	chr4:47928600-47928800	Active TSS	Gastric	stomach
37	chr4:47928600-47928800	Enhancers	Pancreas	Pancrea
38	chr4:47928600-47928800	Enhancers	Right Ventricle	heart
39	chr4:47928600-47928800	Enhancers	K562	blood
40	chr4:47928600-47929000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr4:47928600-47929000	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr4:47928600-47929000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:47928600-47929000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr4:47928600-47929000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:47928600-47929000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr4:47928600-47929000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr4:47928600-47929000	Flanking Active TSS	Fetal Lung	lung
48	chr4:47928600-47929000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr4:47928600-47929000	Active TSS	HepG2	liver
50	chr4:47928600-47929200	Enhancers	Primary monocytes fromperipheralblood	blood

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