Variant report

Variant	rs442767
Chromosome Location	chr5:79951496-79951497
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:79949416-79951701	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:79949816-79951683	Raji	blood:	n/a	n/a
3	POLR2A	chr5:79949826-79951549	GM19193	blood:	n/a	n/a
4	POLR2A	chr5:79949794-79951638	MCF-7	breast:	n/a	n/a
5	POLR2A	chr5:79949856-79951727	GM19099	blood:	n/a	n/a
6	WRNIP1	chr5:79950538-79951574	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:79948603-79951714	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:79949736-79951618	GM12878	blood:	n/a	n/a
9	TBP	chr5:79950571-79951542	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:79949908-79951666	U87	brain:	n/a	n/a
11	POLR2A	chr5:79949810-79951741	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:79949192-79951540	K562	blood:	n/a	n/a
13	POLR2A	chr5:79949922-79951758	U87	brain:	n/a	n/a
14	POLR2A	chr5:79949470-79951611	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr5:79950093-79951524	Hela-S3	cervix:	n/a	n/a
16	USF2	chr5:79950891-79951504	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:79949759-79951597	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr5:79949879-79951586	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:79950436-79952011	GM12878	blood:	n/a	n/a
20	POLR2A	chr5:79950034-79951600	HUVEC	blood vessel:	n/a	n/a
21	RFX5	chr5:79950403-79951571	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:79949949-79951709	K562	blood:	n/a	n/a
23	CHD1	chr5:79950461-79951543	GM12878	blood:	n/a	n/a
24	MTA3	chr5:79950405-79951557	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:79949737-79951753	K562	blood:	n/a	n/a
26	ZKSCAN1	chr5:79950317-79951540	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:79949099-79952397	GM12891	blood:	n/a	n/a
28	STAT1	chr5:79951418-79951521	GM12878	blood:	n/a	n/a
29	FOS	chr5:79951341-79951527	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr5:79949873-79951522	NB4	blood:	n/a	n/a
31	POLR2A	chr5:79949356-79951526	Hela-S3	cervix:	n/a	n/a
32	MXI1	chr5:79950042-79951854	GM12878	blood:	n/a	n/a
33	RUNX3	chr5:79949750-79951542	GM12878	blood:	n/a	chr5:79950116-79950131
34	CHD2	chr5:79950129-79951513	Hela-S3	cervix:	n/a	chr5:79950383-79950393
35	POLR2A	chr5:79949800-79951663	HepG2	liver:	n/a	n/a
36	ELK4	chr5:79950527-79951565	Hela-S3	cervix:	n/a	chr5:79950968-79950979
37	POLR2A	chr5:79949819-79951768	GM18505	blood:	n/a	n/a
38	POLR2A	chr5:79949749-79951546	HepG2	liver:	n/a	n/a
39	POLR2A	chr5:79949093-79951774	K562	blood:	n/a	n/a
40	POLR2A	chr5:79949366-79951545	PBDE	blood:	n/a	n/a
41	RELA	chr5:79949877-79951535	GM18951	blood:	n/a	n/a
42	CTCF	chr5:79951400-79951550	GM06990	blood:	n/a	n/a
43	POLR2A	chr5:79949675-79951713	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr5:79949750-79951639	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr5:79949941-79951545	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:79950548..79951545-chr7:5569740..5570286,2	Hela-S3	cervix:
2	chr5:79930876..79933489-chr5:79951399..79953527,2	K562	blood:
3	chr5:79781713..79786255-chr5:79948613..79954295,12	MCF-7	breast:
4	chr5:79782822..79786705-chr5:79948261..79952248,11	MCF-7	breast:
5	chr5:79702114..79706204-chr5:79947823..79953616,8	MCF-7	breast:
6	chr5:79773551..79776073-chr5:79951057..79953387,2	K562	blood:

No data

Variant related genes	Relation type
DHFR	TF binding region
MTRNR2L2	TF binding region
ENSG00000249042	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000039319	Chromatin interaction
ENSG00000152380	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1105524	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1643665	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2115014	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2434329	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs372069	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs380691	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384925	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs408626	0.92[ASN][1000 genomes]
rs443611	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525054	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151603	0.81[ASN][1000 genomes]
rs6151617	0.83[ASN][1000 genomes]
rs861365	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3406922	chr5:79949421-79951969	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs442767	DHFR	Cis_1M	lymphoblastoid	RTeQTL
rs442767	DHFR	cis	Muscle Skeletal	GTEx
rs442767	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs442767	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs442767	DHFR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79948600-79952000	Active TSS	GM12878-XiMat	blood
2	chr5:79949000-79951600	Active TSS	A549	lung
3	chr5:79949200-79951600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr5:79949200-79951600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:79949200-79951600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:79949200-79951600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:79949200-79952000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:79949400-79951600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:79949600-79952000	Active TSS	K562	blood
10	chr5:79950200-79951600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:79950200-79951600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:79950200-79951600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:79950200-79951600	Active TSS	Fetal Muscle Trunk	muscle
14	chr5:79951000-79951600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr5:79951000-79951600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr5:79951000-79951600	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr5:79951000-79951600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:79951000-79951600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:79951000-79951600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr5:79951000-79951600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr5:79951000-79951600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:79951000-79951600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr5:79951000-79951600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr5:79951000-79951600	Flanking Active TSS	NH-A	brain
25	chr5:79951000-79951800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr5:79951000-79951800	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr5:79951000-79951800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr5:79951000-79951800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr5:79951000-79951800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr5:79951000-79951800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:79951000-79951800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:79951000-79951800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:79951000-79951800	Flanking Active TSS	Liver	Liver
34	chr5:79951000-79951800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr5:79951000-79951800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr5:79951000-79952200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:79951000-79952600	Flanking Active TSS	Osteobl	bone
38	chr5:79951200-79951600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:79951200-79951600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr5:79951200-79951600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr5:79951200-79951600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:79951200-79951600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr5:79951200-79951600	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr5:79951200-79951600	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr5:79951200-79951600	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr5:79951200-79951600	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr5:79951200-79951600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr5:79951200-79951600	Flanking Active TSS	Fetal Brain Male	brain
49	chr5:79951200-79951600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr5:79951200-79951600	Flanking Active TSS	Fetal Lung	lung

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