Variant report

Variant	rs4255398
Chromosome Location	chr1:85661813-85661814
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85641812..85644016-chr1:85661347..85664205,2	K562	blood:
2	chr1:85660899..85662912-chr1:86045569..86048259,2	K562	blood:
3	chr1:85660381..85662955-chr1:85716611..85718297,2	K562	blood:
4	chr1:85658898..85664597-chr1:85664894..85668250,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11161556	0.81[EUR][1000 genomes]
rs11583836	0.82[EUR][1000 genomes]
rs12563295	0.84[EUR][1000 genomes]
rs17122364	0.81[EUR][1000 genomes]
rs17123650	0.81[EUR][1000 genomes]
rs36006436	0.84[EUR][1000 genomes]
rs4243776	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4907139	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671589	0.81[EUR][1000 genomes]
rs72722607	0.81[EUR][1000 genomes]
rs72722613	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72722616	0.92[EUR][1000 genomes]
rs72722624	0.83[EUR][1000 genomes]
rs72722631	0.84[EUR][1000 genomes]
rs72722638	0.83[EUR][1000 genomes]
rs72722643	0.81[EUR][1000 genomes]
rs7366220	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7511739	0.81[EUR][1000 genomes]
rs930912	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv1792086	chr1:85644478-85667608	Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4255398	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus
2	chr1:85627400-85663000	Weak transcription	NHEK	skin
3	chr1:85627800-85664400	Weak transcription	Osteobl	bone
4	chr1:85639000-85665400	Weak transcription	Placenta	Placenta
5	chr1:85644200-85664400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:85645800-85663800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:85646000-85664800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:85646200-85663600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:85646600-85665200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:85646800-85663800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:85647200-85664400	Weak transcription	Fetal Kidney	kidney
12	chr1:85648400-85665200	Weak transcription	Ovary	ovary
13	chr1:85648400-85665200	Weak transcription	HSMM	muscle
14	chr1:85648800-85664600	Weak transcription	NH-A	brain
15	chr1:85649200-85665800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:85653600-85664200	Weak transcription	HMEC	breast
17	chr1:85654000-85664800	Weak transcription	HUVEC	blood vessel
18	chr1:85654000-85665600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:85654400-85665600	Weak transcription	Brain Substantia Nigra	brain
20	chr1:85654400-85665800	Weak transcription	Gastric	stomach
21	chr1:85654400-85665800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:85654800-85664600	Weak transcription	Colonic Mucosa	Colon
23	chr1:85654800-85665600	Weak transcription	Pancreas	Pancrea
24	chr1:85656000-85664000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:85656000-85664600	Weak transcription	Fetal Stomach	stomach
26	chr1:85656000-85664600	Weak transcription	NHLF	lung
27	chr1:85656000-85665600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:85656200-85663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:85656200-85663800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:85656200-85663800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:85656200-85663800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:85656200-85664200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:85656200-85664600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:85656200-85664600	Weak transcription	Fetal Intestine Small	intestine
35	chr1:85656200-85665800	Weak transcription	Lung	lung
36	chr1:85656400-85662000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:85656400-85662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:85656400-85663400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:85656400-85663600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:85656400-85663600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:85656400-85663600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:85656400-85663600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:85656400-85663800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:85656400-85663800	Weak transcription	Fetal Lung	lung
45	chr1:85656400-85664600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:85656400-85665200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:85656400-85665400	Weak transcription	HSMMtube	muscle
48	chr1:85656400-85665600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:85659400-85663600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:85659600-85663800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links