Variant report

Variant	rs4801960
Chromosome Location	chr19:39424653-39424654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10410544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10416055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10425217	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10426382	1.00[JPT][hapmap]
rs10775533	0.85[ASN][1000 genomes]
rs11083489	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668245	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12462710	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12972986	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12979755	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12982957	0.82[EUR][1000 genomes]
rs17545254	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1808661	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1808662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1865047	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1865049	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs3136640	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs4801971	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4802998	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4803006	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4803034	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7257007	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs730078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7508411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508539	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9636109	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9749516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4801960	CTC-360G5.9	cis	Artery Tibial	GTEx
rs4801960	SARS2	cis	multi-tissue	Pritchard
rs4801960	CTC-360G5.9	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:39422400-39434600	Weak transcription	Fetal Kidney	kidney
3	chr19:39422400-39435000	Weak transcription	Fetal Lung	lung
4	chr19:39422400-39435000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
6	chr19:39422600-39425200	Weak transcription	Primary B cells from cord blood	blood
7	chr19:39422600-39425200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:39422600-39425200	Weak transcription	Stomach Mucosa	stomach
9	chr19:39422600-39427000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:39422600-39430200	Weak transcription	HUVEC	blood vessel
11	chr19:39422600-39430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:39422600-39435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:39422600-39435200	Weak transcription	HSMM	muscle
14	chr19:39422600-39440200	Weak transcription	NH-A	brain
15	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
17	chr19:39422800-39424800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:39422800-39425200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:39422800-39425400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:39422800-39425600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:39422800-39432600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:39423000-39424800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39423000-39424800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:39423000-39424800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:39423000-39424800	Strong transcription	Brain Substantia Nigra	brain
26	chr19:39423000-39424800	Strong transcription	Fetal Thymus	thymus
27	chr19:39423000-39425200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:39423000-39425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:39423000-39425200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr19:39423000-39425400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr19:39423000-39425400	Strong transcription	Fetal Stomach	stomach
32	chr19:39423000-39425600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:39423000-39425800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39423000-39425800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr19:39423000-39425800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:39423000-39425800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr19:39423200-39424800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39423200-39424800	Strong transcription	NHEK	skin
39	chr19:39423200-39425000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39423200-39425200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:39423200-39425400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:39423200-39425400	Strong transcription	Placenta	Placenta
43	chr19:39423200-39425600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39423200-39425800	Strong transcription	Primary T cells from cord blood	blood
45	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
46	chr19:39423400-39424800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:39423400-39424800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:39423400-39424800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:39423400-39425400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:39423400-39425400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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