Variant report

Variant	rs4890628
Chromosome Location	chr18:43788045-43788046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43753779..43755343-chr18:43787383..43789428,2	MCF-7	breast:
2	chr18:43752117..43755580-chr18:43786851..43790575,4	K562	blood:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

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]
rs11082514	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11082518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12457740	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12604963	0.81[ASN][1000 genomes]
rs12605275	0.81[ASN][1000 genomes]
rs12605945	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]
rs12607898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12608232	0.92[EUR][1000 genomes]
rs12709736	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12953780	0.83[ASN][1000 genomes]
rs12954967	0.81[ASN][1000 genomes]
rs12962307	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]
rs12962951	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12963787	0.95[EUR][1000 genomes]
rs12963943	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12965578	0.81[ASN][1000 genomes]
rs12967694	0.87[CHB][hapmap]
rs12969147	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]
rs13381496	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13381515	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13381523	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13381525	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13381529	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16978526	0.81[ASN][1000 genomes]
rs16978530	0.80[ASN][1000 genomes]
rs1791407	0.81[JPT][hapmap]
rs1791413	0.81[JPT][hapmap]
rs1791414	0.81[JPT][hapmap]
rs1808946	0.95[EUR][1000 genomes]
rs36191490	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3744858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4243279	0.81[ASN][1000 genomes]
rs4335852	0.92[EUR][1000 genomes]
rs4453594	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4453596	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4542747	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4574015	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs4627465	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890317	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs4890319	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890320	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890321	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890626	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4890629	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890631	0.95[EUR][1000 genomes]
rs4890632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890633	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4890634	0.93[EUR][1000 genomes]
rs55747741	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62096523	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62096524	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62096525	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62096526	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62098160	0.90[EUR][1000 genomes]
rs6507670	0.81[EUR][1000 genomes]
rs6507675	0.80[CHB][hapmap]
rs6507676	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6507677	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6507679	0.81[JPT][hapmap]
rs6507680	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507681	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6507682	0.92[EUR][1000 genomes]
rs6507690	0.97[EUR][1000 genomes]
rs6507691	0.95[EUR][1000 genomes]
rs6507692	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6507693	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs718513	0.87[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs718514	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7227847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7228024	0.85[ASN][1000 genomes]
rs7228365	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs7230154	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs7230905	0.83[ASN][1000 genomes]
rs7230995	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7231430	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7231820	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234695	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7236687	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7239351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7240354	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7241527	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7241829	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7242375	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7245091	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73425119	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7506126	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs8084309	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8084827	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8084829	0.96[EUR][1000 genomes]
rs8085138	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8086610	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8086956	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8090542	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8093407	0.95[EUR][1000 genomes]
rs8094070	0.95[EUR][1000 genomes]
rs8094706	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8095142	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8095729	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8095799	0.96[EUR][1000 genomes]
rs8098751	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8099202	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9675387	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs9807157	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9944715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9944767	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs9944836	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs9945783	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9947206	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9948282	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9949494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9951624	0.95[EUR][1000 genomes]
rs9952469	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]
rs9952654	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9956574	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9959526	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9959813	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs9959905	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs9960378	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9963153	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs9963843	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs9967229	0.81[JPT][hapmap];0.81[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
rs4890628	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43755600-43795600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr18:43756800-43796000	Weak transcription	Esophagus	oesophagus
3	chr18:43761200-43796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:43763000-43795800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr18:43763400-43799200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr18:43763600-43796000	Weak transcription	Fetal Lung	lung
7	chr18:43764600-43795800	Weak transcription	Lung	lung
8	chr18:43769200-43802800	Weak transcription	Brain Hippocampus Middle	brain
9	chr18:43770800-43796000	Weak transcription	Brain Substantia Nigra	brain
10	chr18:43771800-43795800	Weak transcription	Brain Anterior Caudate	brain
11	chr18:43772000-43795800	Weak transcription	Adipose Nuclei	Adipose
12	chr18:43772000-43795800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr18:43772200-43796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr18:43772800-43795800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr18:43774400-43795800	Weak transcription	Fetal Stomach	stomach
16	chr18:43776400-43802000	Weak transcription	Brain Germinal Matrix	brain
17	chr18:43776800-43795800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr18:43777000-43812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:43777200-43791600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr18:43777200-43795600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr18:43777800-43795800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:43777800-43805000	Weak transcription	Fetal Intestine Small	intestine
23	chr18:43778200-43789200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr18:43778600-43788400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr18:43780000-43791400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:43780000-43791400	Weak transcription	Osteobl	bone
27	chr18:43780000-43793200	Weak transcription	Liver	Liver
28	chr18:43780000-43795800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr18:43780200-43793200	Weak transcription	Fetal Heart	heart
30	chr18:43780400-43791400	Weak transcription	K562	blood
31	chr18:43780600-43790600	Weak transcription	Left Ventricle	heart
32	chr18:43780800-43790600	Weak transcription	Psoas Muscle	Psoas
33	chr18:43781200-43791400	Weak transcription	Hela-S3	cervix
34	chr18:43781400-43795200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr18:43782000-43789400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr18:43783000-43788200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr18:43783000-43789000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr18:43783000-43790600	Weak transcription	Right Ventricle	heart
39	chr18:43783400-43793200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr18:43783600-43796000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr18:43784600-43795800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr18:43784600-43802200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr18:43784800-43790800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr18:43784800-43791200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr18:43784800-43795800	Weak transcription	HSMMtube	muscle
46	chr18:43784800-43796000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr18:43784800-43796000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr18:43784800-43796000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr18:43785000-43791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr18:43785200-43796000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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