Variant report

Variant	rs280597
Chromosome Location	chr4:129944209-129944210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10028974	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11098994	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs172168	0.95[ASN][1000 genomes]
rs1756011	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1757926	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757929	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757937	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757938	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757942	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1838911	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs189236	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2118045	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592948	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2597837	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2655311	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777822	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777823	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280594	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280596	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280601	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3099902	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099903	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113487	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113488	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337279	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55865936	0.85[ASN][1000 genomes]
rs62316971	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62316978	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7654405	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs796886	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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
rs280597	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs280597	C4orf33	cis	Artery Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129932200-129947000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:129935800-129944400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:129937200-129964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:129937800-129947000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:129941200-129945600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:129941200-129945800	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:129941400-129944400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr4:129941400-129945000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:129942000-129944600	ZNF genes & repeats	Fetal Muscle Leg	muscle
10	chr4:129942200-129944600	ZNF genes & repeats	Dnd41	blood
11	chr4:129942200-129944800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:129942200-129945200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr4:129942400-129944400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr4:129942400-129944800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr4:129942400-129944800	ZNF genes & repeats	Liver	Liver
16	chr4:129942600-129944600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:129942800-129944800	Weak transcription	Gastric	stomach
18	chr4:129942800-129952200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:129943000-129944600	Weak transcription	Ovary	ovary
20	chr4:129943200-129944400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:129943200-129944400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:129943200-129944400	Weak transcription	Left Ventricle	heart
23	chr4:129943200-129944800	Weak transcription	Pancreas	Pancrea
24	chr4:129943200-129954600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:129943200-129960200	Weak transcription	Primary B cells from cord blood	blood
26	chr4:129943400-129944600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
27	chr4:129943400-129944600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
28	chr4:129943600-129944400	ZNF genes & repeats	Primary T cells from cord blood	blood
29	chr4:129943600-129944400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
30	chr4:129943600-129944800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr4:129943600-129944800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
32	chr4:129943600-129945000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:129943800-129944400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
34	chr4:129943800-129944800	ZNF genes & repeats	Adipose Nuclei	Adipose
35	chr4:129944200-129944600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
36	chr4:129944200-129944600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:129944200-129944800	ZNF genes & repeats	Fetal Lung	lung
38	chr4:129944200-129945600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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