Variant report

Variant	rs12962307
Chromosome Location	chr18:43815420-43815421
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43813159..43815457-chr18:43822557..43825272,2	K562	blood:

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	0.88[AFR][1000 genomes];0.90[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];0.97[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];0.95[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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12608232	0.92[EUR][1000 genomes]
rs12709736	0.94[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]
rs12962951	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12963787	0.97[EUR][1000 genomes]
rs12963943	0.94[AFR][1000 genomes];0.96[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];0.94[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	0.97[EUR][1000 genomes]
rs36191490	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3744858	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]
rs4243279	0.83[ASN][1000 genomes]
rs4274509	0.83[JPT][hapmap]
rs4335852	0.92[EUR][1000 genomes]
rs4453594	0.96[EUR][1000 genomes]
rs4453596	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4542747	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4574015	0.95[CEU][hapmap];0.81[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];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4890320	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4890321	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890626	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[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];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890631	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890633	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4890634	0.82[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	0.90[EUR][1000 genomes]
rs6507679	0.86[JPT][hapmap]
rs6507680	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6507681	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6507682	0.92[EUR][1000 genomes]
rs6507690	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6507691	0.96[EUR][1000 genomes]
rs6507692	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6507693	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs718513	0.87[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718514	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7227847	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7228024	0.82[ASN][1000 genomes]
rs7228365	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7230154	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs7230905	0.81[ASN][1000 genomes]
rs7230995	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7231430	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7231820	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[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];0.84[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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7240354	0.89[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];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8084827	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8084829	0.95[EUR][1000 genomes]
rs8085138	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8086610	0.94[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];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8090542	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093407	0.97[EUR][1000 genomes]
rs8094070	0.97[EUR][1000 genomes]
rs8094706	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8095142	0.88[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	0.95[EUR][1000 genomes]
rs8098751	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8099202	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9675387	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9807157	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9944715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[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];0.98[EUR][1000 genomes]
rs9945783	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9947206	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9948282	0.95[EUR][1000 genomes]
rs9949494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9951624	0.97[EUR][1000 genomes]
rs9952469	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]
rs9952654	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9956574	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs9959526	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9959813	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs9959905	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs9960378	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9963153	0.95[CEU][hapmap];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
rs12962307	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43796600-43820000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:43796600-43827600	Weak transcription	Fetal Muscle Leg	muscle
3	chr18:43797000-43820000	Weak transcription	Ovary	ovary
4	chr18:43797000-43833400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:43797400-43829600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr18:43798800-43833800	Weak transcription	HepG2	liver
7	chr18:43799000-43834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:43800800-43829000	Weak transcription	HSMM	muscle
9	chr18:43801200-43829600	Weak transcription	Thymus	Thymus
10	chr18:43802800-43828200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr18:43802800-43830000	Weak transcription	Brain Substantia Nigra	brain
12	chr18:43803000-43820000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr18:43803600-43827800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr18:43803800-43820000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr18:43804400-43820000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr18:43804400-43820000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:43804400-43825200	Weak transcription	Hela-S3	cervix
18	chr18:43804600-43825200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr18:43804800-43829400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr18:43805200-43828200	Weak transcription	GM12878-XiMat	blood
21	chr18:43805400-43827600	Weak transcription	Fetal Thymus	thymus
22	chr18:43805400-43829800	Weak transcription	Fetal Intestine Large	intestine
23	chr18:43805600-43820000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr18:43805600-43826200	Weak transcription	Fetal Stomach	stomach
25	chr18:43806200-43826200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr18:43806400-43827600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr18:43806400-43829000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr18:43806800-43818000	Weak transcription	Osteobl	bone
29	chr18:43807400-43818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr18:43808200-43828800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr18:43810000-43829000	Weak transcription	Esophagus	oesophagus
32	chr18:43810200-43821400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr18:43810200-43825200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr18:43810200-43828000	Weak transcription	Lung	lung
35	chr18:43810200-43829400	Weak transcription	Fetal Intestine Small	intestine
36	chr18:43810200-43832400	Weak transcription	Aorta	Aorta
37	chr18:43810400-43827800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr18:43812200-43816800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr18:43814200-43815600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr18:43814400-43815600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:43814400-43815800	Strong transcription	Primary B cells from cord blood	blood
42	chr18:43814400-43815800	Enhancers	Primary T cells from cord blood	blood
43	chr18:43814400-43816000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr18:43814600-43815600	Enhancers	Fetal Heart	heart
45	chr18:43814600-43815600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr18:43814600-43815600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr18:43814600-43815800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr18:43814600-43815800	Enhancers	Stomach Mucosa	stomach
49	chr18:43814600-43816000	Enhancers	Brain Anterior Caudate	brain
50	chr18:43814600-43816400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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