Variant report

Variant	rs62096524
Chromosome Location	chr18:43738027-43738028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43731824..43733616-chr18:43737124..43738884,2	MCF-7	breast:
2	chr18:43737408..43740388-chr18:43753340..43756305,2	MCF-7	breast:
3	chr18:43737274..43740808-chr18:43743421..43745536,3	K562	blood:
4	chr18:43737434..43740095-chr18:43752328..43754121,3	MCF-7	breast:
5	chr18:43737450..43741302-chr18:43741650..43744283,3	MCF-7	breast:
6	chr18:43736114..43739011-chr18:43760662..43762501,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs11082512	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11082514	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11082518	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12457740	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12605945	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12607898	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12608232	0.85[EUR][1000 genomes]
rs12709736	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12962307	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12962951	0.85[EUR][1000 genomes]
rs12963787	0.83[EUR][1000 genomes]
rs12963943	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12967694	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12969147	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13381496	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13381515	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13381523	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13381525	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13381529	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1791403	0.82[ASN][1000 genomes]
rs1808946	0.83[EUR][1000 genomes]
rs36191490	0.85[EUR][1000 genomes]
rs3744858	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4335852	0.90[EUR][1000 genomes]
rs4453594	0.85[EUR][1000 genomes]
rs4453596	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4542747	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4574015	0.84[EUR][1000 genomes]
rs4627465	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4890317	0.90[EUR][1000 genomes]
rs4890319	0.85[EUR][1000 genomes]
rs4890320	0.84[EUR][1000 genomes]
rs4890321	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4890628	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4890629	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4890631	0.83[EUR][1000 genomes]
rs4890632	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4890633	0.85[EUR][1000 genomes]
rs4890634	0.81[EUR][1000 genomes]
rs55747741	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62096523	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62096525	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62096526	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6507670	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507676	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507677	0.90[EUR][1000 genomes]
rs6507680	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6507681	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507682	0.90[EUR][1000 genomes]
rs6507690	0.84[EUR][1000 genomes]
rs6507691	0.82[EUR][1000 genomes]
rs6507692	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6507693	0.85[EUR][1000 genomes]
rs718513	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs718514	0.81[EUR][1000 genomes]
rs7227847	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7228365	0.84[EUR][1000 genomes]
rs7230154	0.84[EUR][1000 genomes]
rs7230995	0.85[EUR][1000 genomes]
rs7231430	0.85[EUR][1000 genomes]
rs7231820	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7234695	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7236687	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7239351	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7240354	0.82[ASN][1000 genomes]
rs7241527	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7241829	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7242375	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7245091	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73425119	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8084309	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8084827	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8084829	0.82[EUR][1000 genomes]
rs8085138	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8086610	0.84[EUR][1000 genomes]
rs8086956	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8090542	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8093407	0.83[EUR][1000 genomes]
rs8094070	0.83[EUR][1000 genomes]
rs8094706	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8095142	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8095729	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8095799	0.86[EUR][1000 genomes]
rs8098751	0.83[EUR][1000 genomes]
rs8099202	0.85[EUR][1000 genomes]
rs9675387	0.84[EUR][1000 genomes]
rs9807157	0.84[EUR][1000 genomes]
rs9944715	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9944767	0.80[EUR][1000 genomes]
rs9944836	0.84[EUR][1000 genomes]
rs9945783	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9947206	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9948282	0.87[EUR][1000 genomes]
rs9949494	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9951624	0.83[EUR][1000 genomes]
rs9952469	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9952654	0.84[EUR][1000 genomes]
rs9956574	0.86[EUR][1000 genomes]
rs9959813	0.83[EUR][1000 genomes]
rs9959905	0.84[EUR][1000 genomes]
rs9960378	0.84[EUR][1000 genomes]
rs9963153	0.83[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
rs62096524	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43706200-43747800	Weak transcription	Brain Substantia Nigra	brain
2	chr18:43710600-43752800	Weak transcription	Fetal Brain Female	brain
3	chr18:43712400-43739200	Weak transcription	Fetal Intestine Small	intestine
4	chr18:43714000-43748400	Weak transcription	Ovary	ovary
5	chr18:43732000-43738600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr18:43732600-43739000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr18:43733200-43740200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr18:43733200-43740600	Enhancers	HMEC	breast
9	chr18:43733200-43753200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr18:43733600-43738400	Weak transcription	Fetal Heart	heart
11	chr18:43733600-43738400	Weak transcription	Left Ventricle	heart
12	chr18:43733600-43746200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr18:43733600-43746400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr18:43733800-43738400	Enhancers	Hela-S3	cervix
15	chr18:43733800-43744200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr18:43733800-43746200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr18:43734200-43746200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr18:43734600-43740600	Enhancers	NHEK	skin
19	chr18:43734800-43739400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr18:43735000-43738600	Weak transcription	Psoas Muscle	Psoas
21	chr18:43735000-43739000	Enhancers	Placenta	Placenta
22	chr18:43735600-43739000	Enhancers	K562	blood
23	chr18:43736000-43738600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:43736400-43738600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr18:43736400-43739200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr18:43736400-43740400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr18:43736400-43742400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr18:43736400-43742400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr18:43736400-43747800	Weak transcription	Thymus	Thymus
30	chr18:43736600-43738400	Weak transcription	Osteobl	bone
31	chr18:43736600-43739000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr18:43736600-43739200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr18:43736600-43739200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr18:43736800-43738400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr18:43736800-43738400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr18:43736800-43739400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr18:43736800-43740200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr18:43736800-43740400	Weak transcription	NH-A	brain
39	chr18:43736800-43746200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr18:43737000-43738200	Enhancers	Dnd41	blood
41	chr18:43737000-43738400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr18:43737000-43739000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr18:43737000-43739000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr18:43737200-43738200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr18:43737200-43738200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr18:43737200-43739200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr18:43737200-43747800	Weak transcription	Spleen	Spleen
48	chr18:43737200-43749200	Weak transcription	HSMMtube	muscle
49	chr18:43737200-43749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr18:43737400-43738400	Weak transcription	A549	lung

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