Variant report

Variant	rs9952469
Chromosome Location	chr18:43812010-43812011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs11082512	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11082514	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11082518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457740	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12604963	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12605275	0.84[ASN][1000 genomes]
rs12605945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12608232	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12709736	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12953780	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12954967	0.83[ASN][1000 genomes]
rs12962307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12962951	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12963787	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12963943	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12967694	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs12969147	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13381496	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381515	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381523	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381525	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381529	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16978526	0.84[ASN][1000 genomes]
rs16978530	0.82[ASN][1000 genomes]
rs1791407	0.86[JPT][hapmap]
rs1791413	0.86[JPT][hapmap]
rs1791414	0.86[JPT][hapmap]
rs1808946	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36191490	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3744858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4243279	0.83[ASN][1000 genomes]
rs4274509	0.83[JPT][hapmap]
rs4335852	0.92[EUR][1000 genomes]
rs4453594	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4453596	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4542747	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4574015	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4627465	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890317	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs4890319	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4890320	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4890321	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890626	0.87[EUR][1000 genomes]
rs4890628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890629	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890631	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890633	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4890634	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55747741	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62096523	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62096524	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62096525	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62096526	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62098160	0.91[EUR][1000 genomes]
rs6507670	0.81[EUR][1000 genomes]
rs6507675	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs6507676	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6507677	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6507679	0.86[JPT][hapmap]
rs6507680	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6507681	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6507682	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6507690	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6507691	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6507692	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6507693	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs718513	0.87[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718514	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7227847	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7228024	0.82[ASN][1000 genomes]
rs7228365	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7230154	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7230905	0.81[ASN][1000 genomes]
rs7230995	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7231430	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7231820	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7234695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236687	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7239351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7240354	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7241527	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7241829	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7242375	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7245091	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73425119	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7506126	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8084309	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8084827	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8084829	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8085138	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8086610	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8086956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8090542	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093407	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8094070	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8094706	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8095142	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8095729	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8095799	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8098751	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8099202	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9675387	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9807157	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9944715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944767	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs9944836	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9945783	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9947206	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9948282	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9949494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9951624	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9952654	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9956574	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9959526	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9959813	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9959905	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9960378	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9963153	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9963843	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9967229	0.86[JPT][hapmap];0.83[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	nsv1064031	chr18:43782309-43878806	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9952469	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43792200-43814600	Weak transcription	Colon Smooth Muscle	Colon
2	chr18:43794800-43815000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr18:43796600-43814200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:43796600-43815200	Weak transcription	Pancreas	Pancrea
5	chr18:43796600-43820000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr18:43796600-43827600	Weak transcription	Fetal Muscle Leg	muscle
7	chr18:43796800-43814800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr18:43797000-43814800	Weak transcription	Fetal Brain Female	brain
9	chr18:43797000-43820000	Weak transcription	Ovary	ovary
10	chr18:43797000-43833400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr18:43797400-43829600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr18:43798800-43833800	Weak transcription	HepG2	liver
13	chr18:43799000-43814600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr18:43799000-43834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:43800400-43814400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:43800400-43814600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr18:43800800-43829000	Weak transcription	HSMM	muscle
18	chr18:43801200-43829600	Weak transcription	Thymus	Thymus
19	chr18:43802800-43828200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr18:43802800-43830000	Weak transcription	Brain Substantia Nigra	brain
21	chr18:43803000-43820000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr18:43803600-43827800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr18:43803800-43820000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr18:43804000-43814600	Weak transcription	Brain Anterior Caudate	brain
25	chr18:43804200-43815200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr18:43804400-43820000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr18:43804400-43820000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:43804400-43825200	Weak transcription	Hela-S3	cervix
29	chr18:43804600-43815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:43804600-43825200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr18:43804800-43814400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr18:43804800-43829400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr18:43805200-43814600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr18:43805200-43814800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:43805200-43815200	Weak transcription	HMEC	breast
36	chr18:43805200-43828200	Weak transcription	GM12878-XiMat	blood
37	chr18:43805400-43814600	Weak transcription	Placenta	Placenta
38	chr18:43805400-43814600	Weak transcription	NHEK	skin
39	chr18:43805400-43814800	Weak transcription	Dnd41	blood
40	chr18:43805400-43827600	Weak transcription	Fetal Thymus	thymus
41	chr18:43805400-43829800	Weak transcription	Fetal Intestine Large	intestine
42	chr18:43805600-43814600	Weak transcription	Gastric	stomach
43	chr18:43805600-43820000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr18:43805600-43826200	Weak transcription	Fetal Stomach	stomach
45	chr18:43806200-43826200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr18:43806400-43814400	Weak transcription	Primary B cells from cord blood	blood
47	chr18:43806400-43827600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr18:43806400-43829000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr18:43806800-43818000	Weak transcription	Osteobl	bone
50	chr18:43807400-43818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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