Variant report

Variant	rs55747741
Chromosome Location	chr18:43748913-43748914
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43746724..43751707-chr18:43751917..43755971,9	K562	blood:
2	chr18:43746724..43751269-chr18:43752308..43755984,7	K562	blood:
3	chr18:43746705..43749861-chr18:43753099..43755750,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs11082512	0.86[EUR][1000 genomes]
rs11082514	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11082518	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12457740	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12605945	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12607898	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12608232	0.87[EUR][1000 genomes]
rs12709736	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12962307	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12962951	0.87[EUR][1000 genomes]
rs12963787	0.85[EUR][1000 genomes]
rs12963943	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12967694	0.86[EUR][1000 genomes]
rs12969147	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13381496	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381515	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381523	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381525	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381529	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808946	0.86[EUR][1000 genomes]
rs36191490	0.87[EUR][1000 genomes]
rs3744858	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4335852	0.92[EUR][1000 genomes]
rs4453594	0.87[EUR][1000 genomes]
rs4453596	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4542747	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4574015	0.86[EUR][1000 genomes]
rs4627465	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890317	0.92[EUR][1000 genomes]
rs4890319	0.87[EUR][1000 genomes]
rs4890320	0.86[EUR][1000 genomes]
rs4890321	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890628	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4890629	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890631	0.86[EUR][1000 genomes]
rs4890632	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890633	0.87[EUR][1000 genomes]
rs4890634	0.83[EUR][1000 genomes]
rs62096523	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096524	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62096525	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62096526	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62098160	0.81[EUR][1000 genomes]
rs6507670	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6507675	0.83[ASN][1000 genomes]
rs6507676	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6507677	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6507680	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507681	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507682	0.92[EUR][1000 genomes]
rs6507690	0.87[EUR][1000 genomes]
rs6507691	0.85[EUR][1000 genomes]
rs6507692	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507693	0.87[EUR][1000 genomes]
rs718513	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs718514	0.84[EUR][1000 genomes]
rs7227847	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7228024	0.81[ASN][1000 genomes]
rs7228365	0.87[EUR][1000 genomes]
rs7230154	0.87[EUR][1000 genomes]
rs7230995	0.87[EUR][1000 genomes]
rs7231430	0.87[EUR][1000 genomes]
rs7231820	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234695	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7236687	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239351	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7240354	0.88[ASN][1000 genomes]
rs7241527	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7241829	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7242375	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245091	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73425119	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8084309	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8084827	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8084829	0.84[EUR][1000 genomes]
rs8085138	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8086610	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8086956	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8090542	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093407	0.86[EUR][1000 genomes]
rs8094070	0.86[EUR][1000 genomes]
rs8094706	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8095142	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8095729	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8095799	0.88[EUR][1000 genomes]
rs8098751	0.85[EUR][1000 genomes]
rs8099202	0.87[EUR][1000 genomes]
rs9675387	0.86[EUR][1000 genomes]
rs9807157	0.87[EUR][1000 genomes]
rs9944715	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9944767	0.83[EUR][1000 genomes]
rs9944836	0.87[EUR][1000 genomes]
rs9945783	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9947206	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9948282	0.89[EUR][1000 genomes]
rs9949494	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9951624	0.86[EUR][1000 genomes]
rs9952469	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9952654	0.85[EUR][1000 genomes]
rs9956574	0.88[EUR][1000 genomes]
rs9959813	0.86[EUR][1000 genomes]
rs9959905	0.87[EUR][1000 genomes]
rs9960378	0.87[EUR][1000 genomes]
rs9963153	0.86[EUR][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	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55747741	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43710600-43752800	Weak transcription	Fetal Brain Female	brain
2	chr18:43733200-43753200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:43737200-43749200	Weak transcription	HSMMtube	muscle
4	chr18:43737200-43749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:43737600-43753000	Weak transcription	Fetal Stomach	stomach
6	chr18:43739000-43753200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr18:43740200-43749200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr18:43740600-43749200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr18:43742200-43749000	Weak transcription	Hela-S3	cervix
10	chr18:43744200-43749200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:43744800-43749000	Weak transcription	K562	blood
12	chr18:43746200-43749600	Enhancers	Primary B cells from peripheral blood	blood
13	chr18:43746600-43749400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr18:43747000-43749200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr18:43747000-43749200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:43747000-43749400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr18:43747000-43753000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr18:43747000-43753000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr18:43747200-43749200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr18:43748000-43749800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr18:43748200-43749200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr18:43748200-43749200	Weak transcription	Brain Substantia Nigra	brain
23	chr18:43748200-43749400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr18:43748200-43749400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:43748200-43749600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:43748200-43751000	Weak transcription	Placenta	Placenta
27	chr18:43748200-43752400	Weak transcription	Dnd41	blood
28	chr18:43748200-43752800	Weak transcription	Fetal Muscle Leg	muscle
29	chr18:43748200-43753000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr18:43748200-43753000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr18:43748200-43753000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr18:43748200-43753000	Weak transcription	Brain Hippocampus Middle	brain
33	chr18:43748200-43753200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr18:43748400-43749200	Enhancers	HepG2	liver
35	chr18:43748400-43749200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr18:43748400-43750000	Enhancers	GM12878-XiMat	blood
37	chr18:43748400-43752600	Weak transcription	Primary B cells from cord blood	blood
38	chr18:43748400-43752600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr18:43748400-43752800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr18:43748400-43752800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr18:43748400-43752800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr18:43748400-43753000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr18:43748400-43753000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr18:43748400-43753000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr18:43748400-43753000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr18:43748400-43753000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr18:43748400-43753000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr18:43748400-43753000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:43748400-43753000	Weak transcription	Adipose Nuclei	Adipose
50	chr18:43748400-43753000	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links