Variant report

Variant	rs4574015
Chromosome Location	chr18:43802126-43802127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43753471..43755560-chr18:43800919..43802940,2	K562	blood:
2	chr18:43795518..43797206-chr18:43801637..43804077,2	K562	blood:
3	chr18:43793217..43797206-chr18:43801637..43804775,4	K562	blood:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11082514	0.91[EUR][1000 genomes]
rs11082518	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs11082519	0.92[ASN][1000 genomes]
rs12457516	0.87[ASN][1000 genomes]
rs12457740	0.85[EUR][1000 genomes]
rs12605945	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs12607898	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12608232	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12709736	0.97[EUR][1000 genomes]
rs12962307	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12962951	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12963787	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963943	0.92[EUR][1000 genomes]
rs12969147	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13381496	0.85[EUR][1000 genomes]
rs13381515	0.87[EUR][1000 genomes]
rs13381523	0.86[EUR][1000 genomes]
rs13381525	0.87[EUR][1000 genomes]
rs13381529	0.87[EUR][1000 genomes]
rs1808946	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36191490	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3744858	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4335852	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4453594	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4453596	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs4542747	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4627465	0.87[EUR][1000 genomes]
rs4890317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4890319	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890320	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890321	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4890626	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890628	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs4890629	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4890631	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890632	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4890633	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890634	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890635	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs55747741	0.86[EUR][1000 genomes]
rs62096523	0.84[EUR][1000 genomes]
rs62096524	0.84[EUR][1000 genomes]
rs62096525	0.86[EUR][1000 genomes]
rs62096526	0.85[EUR][1000 genomes]
rs62098160	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6507670	0.81[EUR][1000 genomes]
rs6507676	0.84[EUR][1000 genomes]
rs6507677	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6507680	0.92[EUR][1000 genomes]
rs6507681	0.86[EUR][1000 genomes]
rs6507682	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6507690	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6507691	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6507692	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6507693	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718513	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs718514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7227847	0.96[EUR][1000 genomes]
rs7228365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230995	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7231430	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7231820	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7234695	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs7236687	0.83[EUR][1000 genomes]
rs7239351	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7240354	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7241527	0.83[EUR][1000 genomes]
rs7241829	0.83[EUR][1000 genomes]
rs7242375	0.80[EUR][1000 genomes]
rs7245091	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs73425119	0.86[EUR][1000 genomes]
rs8084309	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs8084827	0.85[EUR][1000 genomes]
rs8084829	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8085138	0.92[EUR][1000 genomes]
rs8086610	0.95[EUR][1000 genomes]
rs8086956	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs8090542	0.92[EUR][1000 genomes]
rs8093407	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8094070	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8094706	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs8095142	0.94[EUR][1000 genomes]
rs8095729	0.85[EUR][1000 genomes]
rs8095799	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8098751	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8099202	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9675387	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944715	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs9944767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9945783	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs9947206	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9948282	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949494	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9951624	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9952469	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9952654	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9956574	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9959813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9959905	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9960378	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9963153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9963843	0.95[CEU][hapmap]

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
rs4574015	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43769200-43802800	Weak transcription	Brain Hippocampus Middle	brain
2	chr18:43777000-43812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr18:43777800-43805000	Weak transcription	Fetal Intestine Small	intestine
4	chr18:43784600-43802200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:43791600-43804200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:43792200-43814600	Weak transcription	Colon Smooth Muscle	Colon
7	chr18:43794800-43802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr18:43794800-43802600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr18:43794800-43815000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr18:43796400-43806400	Weak transcription	Small Intestine	intestine
11	chr18:43796600-43802200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr18:43796600-43802400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr18:43796600-43803000	Weak transcription	Brain Angular Gyrus	brain
14	chr18:43796600-43803000	Weak transcription	Right Atrium	heart
15	chr18:43796600-43803200	Weak transcription	HUVEC	blood vessel
16	chr18:43796600-43803600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr18:43796600-43804000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr18:43796600-43804800	Weak transcription	Gastric	stomach
19	chr18:43796600-43804800	Weak transcription	Left Ventricle	heart
20	chr18:43796600-43809600	Weak transcription	Aorta	Aorta
21	chr18:43796600-43809600	Weak transcription	Esophagus	oesophagus
22	chr18:43796600-43809600	Weak transcription	Lung	lung
23	chr18:43796600-43809600	Weak transcription	Spleen	Spleen
24	chr18:43796600-43814200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr18:43796600-43815200	Weak transcription	Pancreas	Pancrea
26	chr18:43796600-43820000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr18:43796600-43827600	Weak transcription	Fetal Muscle Leg	muscle
28	chr18:43796800-43804800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:43796800-43804800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr18:43796800-43814800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr18:43797000-43802800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr18:43797000-43804200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr18:43797000-43804800	Weak transcription	Fetal Intestine Large	intestine
34	chr18:43797000-43804800	Weak transcription	Placenta	Placenta
35	chr18:43797000-43806200	Weak transcription	Liver	Liver
36	chr18:43797000-43814800	Weak transcription	Fetal Brain Female	brain
37	chr18:43797000-43820000	Weak transcription	Ovary	ovary
38	chr18:43797000-43833400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr18:43797200-43803600	Weak transcription	Hela-S3	cervix
40	chr18:43797400-43829600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr18:43797600-43802800	Weak transcription	Fetal Lung	lung
42	chr18:43798800-43833800	Weak transcription	HepG2	liver
43	chr18:43799000-43802200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr18:43799000-43803600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr18:43799000-43804000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr18:43799000-43804800	Weak transcription	Fetal Thymus	thymus
47	chr18:43799000-43805000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr18:43799000-43814600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr18:43799000-43834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr18:43799200-43802600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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