Variant report

Variant	rs12709736
Chromosome Location	chr18:43793215-43793216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43792629..43794429-chr18:43796211..43797949,2	K562	blood:
2	chr18:43728638..43729142-chr18:43793049..43793799,2	MCF-7	breast:
3	chr18:43792929..43795113-chr18:43795135..43797949,3	K562	blood:
4	chr18:43753194..43756056-chr18:43792065..43794943,3	MCF-7	breast:
5	chr18:43753062..43754536-chr18:43793045..43793982,8	MCF-7	breast:
6	chr18:43753206..43754032-chr18:43793047..43793998,3	MCF-7	breast:
7	chr18:43732879..43733480-chr18:43792915..43793543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs11082514	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11082518	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12457740	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12604963	0.81[ASN][1000 genomes]
rs12605275	0.81[ASN][1000 genomes]
rs12605945	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12607898	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12608232	0.92[EUR][1000 genomes]
rs12954967	0.82[ASN][1000 genomes]
rs12962307	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12962951	0.97[EUR][1000 genomes]
rs12963787	0.95[EUR][1000 genomes]
rs12963943	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12969147	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13381496	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381515	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381523	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381525	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381529	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16978526	0.81[ASN][1000 genomes]
rs16978530	0.81[ASN][1000 genomes]
rs1808946	0.95[EUR][1000 genomes]
rs36191490	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3744858	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243279	0.82[ASN][1000 genomes]
rs4335852	0.91[EUR][1000 genomes]
rs4453594	0.97[EUR][1000 genomes]
rs4453596	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4542747	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4574015	0.97[EUR][1000 genomes]
rs4627465	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890317	0.91[EUR][1000 genomes]
rs4890319	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890320	0.96[EUR][1000 genomes]
rs4890321	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4890626	0.87[EUR][1000 genomes]
rs4890628	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890629	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890631	0.95[EUR][1000 genomes]
rs4890632	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4890633	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890634	0.92[EUR][1000 genomes]
rs55747741	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62096523	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62096524	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62096525	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62096526	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62098160	0.90[EUR][1000 genomes]
rs6507670	0.81[EUR][1000 genomes]
rs6507676	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6507677	0.90[EUR][1000 genomes]
rs6507680	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6507681	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6507682	0.91[EUR][1000 genomes]
rs6507690	0.96[EUR][1000 genomes]
rs6507691	0.94[EUR][1000 genomes]
rs6507692	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6507693	0.97[EUR][1000 genomes]
rs718513	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718514	0.93[EUR][1000 genomes]
rs7227847	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7228024	0.83[ASN][1000 genomes]
rs7228365	0.96[EUR][1000 genomes]
rs7230154	0.96[EUR][1000 genomes]
rs7230905	0.80[ASN][1000 genomes]
rs7230995	0.97[EUR][1000 genomes]
rs7231430	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7231820	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7234695	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236687	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7239351	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7240354	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7241527	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7241829	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7242375	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7245091	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73425119	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7506126	0.81[ASN][1000 genomes]
rs8084309	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8084827	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8084829	0.97[EUR][1000 genomes]
rs8085138	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8086610	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8086956	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8090542	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093407	0.95[EUR][1000 genomes]
rs8094070	0.95[EUR][1000 genomes]
rs8094706	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8095142	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8095729	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8095799	0.95[EUR][1000 genomes]
rs8098751	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8099202	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9675387	0.97[EUR][1000 genomes]
rs9807157	0.96[EUR][1000 genomes]
rs9944715	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9944767	0.92[EUR][1000 genomes]
rs9944836	0.96[EUR][1000 genomes]
rs9945783	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9947206	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9948282	0.94[EUR][1000 genomes]
rs9949494	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9951624	0.95[EUR][1000 genomes]
rs9952469	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9952654	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9956574	0.95[EUR][1000 genomes]
rs9959526	0.82[ASN][1000 genomes]
rs9959813	0.95[EUR][1000 genomes]
rs9959905	0.96[EUR][1000 genomes]
rs9960378	0.96[EUR][1000 genomes]
rs9963153	0.95[EUR][1000 genomes]
rs9967229	0.82[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
rs12709736	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

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	chr18:43777200-43795600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr18:43777800-43795800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:43777800-43805000	Weak transcription	Fetal Intestine Small	intestine
22	chr18:43780000-43795800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr18:43781400-43795200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr18:43783600-43796000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr18:43784600-43795800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr18:43784600-43802200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:43784800-43795800	Weak transcription	HSMMtube	muscle
28	chr18:43784800-43796000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr18:43784800-43796000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr18:43784800-43796000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr18:43785200-43796000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr18:43785400-43795800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr18:43785400-43795800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr18:43785400-43796000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:43786000-43795800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr18:43786800-43796000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:43787000-43795800	Weak transcription	Right Atrium	heart
38	chr18:43789000-43795800	Weak transcription	Fetal Brain Female	brain
39	chr18:43789200-43795200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr18:43789200-43795800	Weak transcription	Placenta	Placenta
41	chr18:43789400-43796200	Weak transcription	A549	lung
42	chr18:43789800-43795000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr18:43790000-43793400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr18:43790200-43795000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr18:43790400-43795000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr18:43790600-43794800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr18:43790800-43794000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr18:43790800-43795000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr18:43791000-43793400	Enhancers	Primary hematopoietic stem cells	blood
50	chr18:43791000-43795000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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