Variant report

Variant	rs12969147
Chromosome Location	chr18:43806524-43806525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43806366..43808522-chr18:43815880..43817704,2	MCF-7	breast:

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	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11082518	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]
rs12457740	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12604963	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12605275	0.83[ASN][1000 genomes]
rs12605945	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607898	0.95[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]
rs12608232	0.92[EUR][1000 genomes]
rs12709736	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12953780	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12954967	0.84[ASN][1000 genomes]
rs12962307	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]
rs12962951	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12963787	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12963943	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12967694	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs13381496	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13381515	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13381523	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13381525	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13381529	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16978526	0.83[ASN][1000 genomes]
rs16978530	0.83[ASN][1000 genomes]
rs1791407	0.86[JPT][hapmap]
rs1791413	0.86[JPT][hapmap]
rs1791414	0.86[JPT][hapmap]
rs1808946	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36191490	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3744858	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4243279	0.84[ASN][1000 genomes]
rs4274509	0.83[JPT][hapmap]
rs4335852	0.92[EUR][1000 genomes]
rs4453594	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4453596	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4542747	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]
rs4574015	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4627465	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4890317	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4890319	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4890320	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4890321	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890626	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs4890628	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890631	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890632	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890633	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4890634	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55747741	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62096523	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62096524	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62096525	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62096526	0.86[EUR][1000 genomes];0.90[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];0.89[ASN][1000 genomes]
rs6507677	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6507679	0.86[JPT][hapmap]
rs6507680	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6507681	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507682	0.92[EUR][1000 genomes]
rs6507690	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6507691	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6507692	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6507693	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs718513	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718514	0.95[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7227847	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7228024	0.84[ASN][1000 genomes]
rs7228365	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7230154	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7230905	0.82[ASN][1000 genomes]
rs7230995	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7231430	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7231820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7234695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7236687	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7239351	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7240354	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7241527	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7241829	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7242375	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7245091	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73425119	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7506126	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8084309	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8084827	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8084829	0.95[EUR][1000 genomes]
rs8085138	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8086610	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8086956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8090542	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8093407	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8094070	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8094706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8095142	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8095729	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8095799	0.95[EUR][1000 genomes]
rs8098751	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8099202	0.95[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9675387	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9807157	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9944715	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944767	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9944836	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9945783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9947206	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9948282	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9949494	0.95[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]
rs9951624	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9952469	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]
rs9952654	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9956574	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9959526	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs9959813	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9959905	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9960378	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9963153	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9963843	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9967229	0.86[JPT][hapmap];0.84[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
rs12969147	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43777000-43812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:43792200-43814600	Weak transcription	Colon Smooth Muscle	Colon
3	chr18:43794800-43815000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr18:43796600-43809600	Weak transcription	Aorta	Aorta
5	chr18:43796600-43809600	Weak transcription	Esophagus	oesophagus
6	chr18:43796600-43809600	Weak transcription	Lung	lung
7	chr18:43796600-43809600	Weak transcription	Spleen	Spleen
8	chr18:43796600-43814200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:43796600-43815200	Weak transcription	Pancreas	Pancrea
10	chr18:43796600-43820000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:43796600-43827600	Weak transcription	Fetal Muscle Leg	muscle
12	chr18:43796800-43814800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr18:43797000-43814800	Weak transcription	Fetal Brain Female	brain
14	chr18:43797000-43820000	Weak transcription	Ovary	ovary
15	chr18:43797000-43833400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr18:43797400-43829600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr18:43798800-43833800	Weak transcription	HepG2	liver
18	chr18:43799000-43814600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr18:43799000-43834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:43800400-43810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr18:43800400-43814400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:43800400-43814600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr18:43800800-43829000	Weak transcription	HSMM	muscle
24	chr18:43801200-43807000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr18:43801200-43829600	Weak transcription	Thymus	Thymus
26	chr18:43802800-43828200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr18:43802800-43830000	Weak transcription	Brain Substantia Nigra	brain
28	chr18:43803000-43807400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:43803000-43820000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:43803200-43806600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr18:43803600-43809800	Weak transcription	Right Atrium	heart
32	chr18:43803600-43827800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr18:43803800-43820000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr18:43804000-43814600	Weak transcription	Brain Anterior Caudate	brain
35	chr18:43804200-43806800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr18:43804200-43815200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr18:43804400-43810000	Weak transcription	Fetal Heart	heart
38	chr18:43804400-43820000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr18:43804400-43820000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr18:43804400-43825200	Weak transcription	Hela-S3	cervix
41	chr18:43804600-43807800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr18:43804600-43815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr18:43804600-43825200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:43804800-43807200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr18:43804800-43807600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr18:43804800-43814400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr18:43804800-43829400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr18:43805000-43808400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr18:43805000-43809800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr18:43805200-43807400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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