Variant report

Variant	rs255529
Chromosome Location	chr5:154216301-154216302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154215310..154217666-chr5:154238733..154240516,2	K562	blood:
2	chr5:154207634..154212086-chr5:154212438..154216728,14	MCF-7	breast:
3	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:
4	chr5:154133720..154135863-chr5:154214585..154216471,2	K562	blood:
5	chr5:154209529..154211376-chr5:154214452..154217277,2	K562	blood:
6	chr5:154214026..154216712-chr5:154234654..154237422,2	K562	blood:

Variant related genes	Relation type
ENSG00000263361	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1035368	0.82[ASN][1000 genomes]
rs11167705	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs158134	0.86[ASN][1000 genomes]
rs17116442	0.86[ASN][1000 genomes]
rs1974776	0.82[ASN][1000 genomes]
rs1974777	0.82[ASN][1000 genomes]
rs2042168	0.82[ASN][1000 genomes]
rs2161128	0.82[ASN][1000 genomes]
rs2258437	0.81[ASN][1000 genomes]
rs2431184	0.83[ASN][1000 genomes]
rs2544860	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544866	0.82[ASN][1000 genomes]
rs2544875	0.86[ASN][1000 genomes]
rs2544880	0.86[ASN][1000 genomes]
rs2644743	0.82[ASN][1000 genomes]
rs2688186	0.86[ASN][1000 genomes]
rs2688188	0.86[ASN][1000 genomes]
rs2688191	0.86[ASN][1000 genomes]
rs2688193	0.86[ASN][1000 genomes]
rs2688200	0.84[ASN][1000 genomes]
rs2688201	0.84[ASN][1000 genomes]
rs286624	0.86[ASN][1000 genomes]
rs348739	0.82[ASN][1000 genomes]
rs348750	0.82[ASN][1000 genomes]
rs348751	0.82[ASN][1000 genomes]
rs348752	0.82[ASN][1000 genomes]
rs348754	0.82[ASN][1000 genomes]
rs39614	0.84[ASN][1000 genomes]
rs4354100	0.82[ASN][1000 genomes]
rs454161	0.83[ASN][1000 genomes]
rs4958771	0.82[ASN][1000 genomes]
rs56374414	0.82[ASN][1000 genomes]
rs58415346	0.82[ASN][1000 genomes]
rs59525998	0.82[ASN][1000 genomes]
rs6580122	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6873483	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6879277	0.82[ASN][1000 genomes]
rs6884416	0.86[ASN][1000 genomes]
rs702742	0.86[ASN][1000 genomes]
rs73276742	0.82[ASN][1000 genomes]
rs73280705	0.82[ASN][1000 genomes]
rs816717	0.86[ASN][1000 genomes]
rs816718	0.86[ASN][1000 genomes]
rs816720	0.86[ASN][1000 genomes]
rs816734	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs816743	0.81[ASN][1000 genomes]
rs816747	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs960499	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs255529	LARP1	cis	Whole Blood	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
2	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
3	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:154210200-154229000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:154210800-154229000	Weak transcription	Fetal Kidney	kidney
6	chr5:154210800-154229800	Weak transcription	Fetal Thymus	thymus
7	chr5:154211000-154216600	Weak transcription	Fetal Lung	lung
8	chr5:154211200-154217200	Weak transcription	Spleen	Spleen
9	chr5:154211400-154217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:154211400-154221600	Weak transcription	Thymus	Thymus
11	chr5:154211400-154228800	Weak transcription	Fetal Brain Female	brain
12	chr5:154211400-154229400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:154211400-154229400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:154211400-154229800	Weak transcription	Pancreas	Pancrea
15	chr5:154211400-154235800	Weak transcription	Dnd41	blood
16	chr5:154211600-154220400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:154211600-154220600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:154211800-154222600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:154211800-154229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:154211800-154229200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:154212400-154229200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:154212600-154229400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:154212800-154216400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:154214400-154216600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:154214400-154221600	Strong transcription	Fetal Stomach	stomach
26	chr5:154214600-154216600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:154214600-154217200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:154214600-154217200	Weak transcription	Aorta	Aorta
29	chr5:154214600-154217400	Weak transcription	Small Intestine	intestine
30	chr5:154214600-154217800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:154214600-154217800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:154214600-154218200	Enhancers	Fetal Intestine Large	intestine
33	chr5:154214600-154218200	Enhancers	Fetal Intestine Small	intestine
34	chr5:154214600-154220400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:154214600-154220600	Weak transcription	Primary T cells from cord blood	blood
36	chr5:154214600-154229200	Weak transcription	Esophagus	oesophagus
37	chr5:154214600-154229400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:154214600-154229800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:154214800-154217200	Weak transcription	Gastric	stomach
40	chr5:154214800-154217400	Enhancers	Liver	Liver
41	chr5:154214800-154220200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:154214800-154220600	Weak transcription	Right Atrium	heart
43	chr5:154214800-154229400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:154214800-154230000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:154214800-154236400	Weak transcription	GM12878-XiMat	blood
46	chr5:154215000-154216400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:154215000-154217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:154215000-154222600	Weak transcription	Stomach Mucosa	stomach
49	chr5:154215000-154224400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:154215000-154224400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links