Variant report

Variant	rs1757942
Chromosome Location	chr4:130001593-130001594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10028974	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098994	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12503465	0.81[AFR][1000 genomes]
rs172168	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17416706	0.81[AFR][1000 genomes]
rs1756011	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757926	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757929	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757937	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757938	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1838911	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs189236	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2044523	0.81[AFR][1000 genomes]
rs2118045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2592948	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597837	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2655311	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777822	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280594	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280596	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs280597	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280601	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3099902	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099903	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113487	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113488	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs337276	0.81[ASN][1000 genomes]
rs337279	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3980331	0.81[AFR][1000 genomes]
rs55865936	0.89[ASN][1000 genomes]
rs62316971	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62316978	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6845314	0.81[AFR][1000 genomes]
rs6847784	0.81[AFR][1000 genomes]
rs72685321	0.81[AFR][1000 genomes]
rs7654405	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1757942	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1757942	C4orf33	cis	Artery Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129983000-130001600	Weak transcription	Fetal Heart	heart
2	chr4:129985200-130002200	Weak transcription	Pancreas	Pancrea
3	chr4:129985200-130012200	Weak transcription	HSMM	muscle
4	chr4:129985200-130013000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:129985200-130013200	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:129987000-130011600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:129990400-130004000	Weak transcription	Right Ventricle	heart
8	chr4:129991600-130011800	Weak transcription	Hela-S3	cervix
9	chr4:129991800-130012000	Weak transcription	HUVEC	blood vessel
10	chr4:129992200-130003600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:129992200-130005400	Weak transcription	Psoas Muscle	Psoas
12	chr4:129992600-130005800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:129992600-130012000	Weak transcription	HepG2	liver
14	chr4:129993000-130007600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:129993000-130012000	Weak transcription	Stomach Mucosa	stomach
16	chr4:129995600-130002800	Weak transcription	NHDF-Ad	bronchial
17	chr4:129995600-130011400	Weak transcription	A549	lung
18	chr4:129997200-130012000	Weak transcription	NHEK	skin
19	chr4:129997600-130002400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:129997600-130010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:129998800-130003000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr4:129998800-130003000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:129998800-130003000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:129999000-130002800	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr4:129999000-130002800	ZNF genes & repeats	Fetal Brain Female	brain
26	chr4:129999000-130003000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:129999000-130003000	Strong transcription	Primary T cells from cord blood	blood
28	chr4:129999000-130003000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:129999000-130003400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:129999000-130008200	ZNF genes & repeats	GM12878-XiMat	blood
31	chr4:129999200-130001600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:129999200-130006400	Weak transcription	Fetal Kidney	kidney
33	chr4:129999200-130012600	Weak transcription	NH-A	brain
34	chr4:129999400-130005400	Weak transcription	Brain Substantia Nigra	brain
35	chr4:129999400-130011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:129999800-130003400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:130000000-130002000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr4:130000000-130002000	ZNF genes & repeats	Fetal Lung	lung
39	chr4:130000000-130002400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:130000000-130002600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:130000000-130002600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:130000000-130002800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:130000000-130002800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:130000000-130002800	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr4:130000000-130002800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:130000000-130003000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr4:130000000-130003000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr4:130000000-130003200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
49	chr4:130000000-130003600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:130000200-130002000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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