Variant report

Variant	rs10003040
Chromosome Location	chr4:84779091-84779092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:84774360..84776816-chr4:84777567..84780524,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10000017	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10011437	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10025543	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10026607	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10027658	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10030289	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10516705	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10516706	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11731734	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12648690	0.81[EUR][1000 genomes]
rs12651425	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13115377	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13126755	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13130476	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138168	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13140768	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1488657	0.94[EUR][1000 genomes]
rs1505786	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1505792	0.96[EUR][1000 genomes]
rs17007624	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1847823	0.94[EUR][1000 genomes]
rs1906578	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2009469	0.93[EUR][1000 genomes]
rs28394381	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28451242	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28780983	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34196281	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34854529	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4524375	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5012041	0.88[EUR][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	nsv879512	chr4:84374692-85090749	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1010009	chr4:84469896-84882528	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv879513	chr4:84612373-84905452	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10003040	COQ2	cis	lymphoblastoid	seeQTL
rs10003040	PLAC8	cis	lymphoblastoid	seeQTL
rs10003040	AGPAT9	cis	lymphoblastoid	seeQTL
rs10003040	PTAFR	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:84773400-84779800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr4:84776600-84781200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:84776600-84785800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:84776800-84780000	Enhancers	A549	lung
5	chr4:84776800-84781000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:84777000-84779200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:84777000-84781600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:84777000-84781600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:84777000-84786600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:84777200-84779200	Weak transcription	NH-A	brain
11	chr4:84777400-84781400	Weak transcription	HSMM	muscle
12	chr4:84777600-84780000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:84778000-84779200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:84778000-84779400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:84778000-84779400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:84778000-84779800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:84778200-84779200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:84778200-84783600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:84778400-84779400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:84778400-84787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:84778600-84787800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:84778800-84779800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:84779000-84779800	Enhancers	Osteobl	bone

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