Variant report

Variant	rs9963153
Chromosome Location	chr18:43840064-43840065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43832515..43836079-chr18:43838698..43841827,4	K562	blood:
2	chr18:43752190..43754856-chr18:43839792..43841964,2	MCF-7	breast:
3	chr18:43838791..43840958-chr18:43849580..43851726,2	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	0.90[EUR][1000 genomes]
rs11082518	0.95[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11082519	0.93[ASN][1000 genomes]
rs12457516	0.88[ASN][1000 genomes]
rs12457740	0.85[EUR][1000 genomes]
rs12605945	0.95[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12607898	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs12608232	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12709736	0.95[EUR][1000 genomes]
rs12962307	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs12962951	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12963787	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12963943	0.89[EUR][1000 genomes]
rs12969147	0.90[CEU][hapmap];0.82[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	0.86[EUR][1000 genomes]
rs13381529	0.87[EUR][1000 genomes]
rs1808946	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36191490	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744858	0.95[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4335852	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4453594	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4453596	0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs4542747	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4574015	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]
rs4627465	0.86[EUR][1000 genomes]
rs4890317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4890319	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890320	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890321	0.95[EUR][1000 genomes]
rs4890626	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890628	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4890629	0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4890631	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890632	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs4890633	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890634	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890635	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs55747741	0.86[EUR][1000 genomes]
rs62096523	0.84[EUR][1000 genomes]
rs62096524	0.83[EUR][1000 genomes]
rs62096525	0.85[EUR][1000 genomes]
rs62096526	0.84[EUR][1000 genomes]
rs62098160	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6507670	0.80[EUR][1000 genomes]
rs6507676	0.84[EUR][1000 genomes]
rs6507677	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507680	0.91[EUR][1000 genomes]
rs6507681	0.84[EUR][1000 genomes]
rs6507682	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507690	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6507691	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6507692	0.97[EUR][1000 genomes]
rs6507693	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718513	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs718514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7227847	0.93[EUR][1000 genomes]
rs7228365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7230154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7230995	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7231430	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231820	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs7234695	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs7236687	0.82[EUR][1000 genomes]
rs7239351	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7240354	0.87[EUR][1000 genomes]
rs7241527	0.82[EUR][1000 genomes]
rs7241829	0.82[EUR][1000 genomes]
rs7242375	0.86[MEX][hapmap];0.89[TSI][hapmap]
rs7245091	0.81[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs73425119	0.86[EUR][1000 genomes]
rs8084309	0.85[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs8084827	0.84[EUR][1000 genomes]
rs8084829	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8085138	0.91[EUR][1000 genomes]
rs8086610	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8086956	0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs8090542	0.91[EUR][1000 genomes]
rs8093407	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8094070	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8094706	0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs8095142	0.92[EUR][1000 genomes]
rs8095729	0.84[EUR][1000 genomes]
rs8095799	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8098751	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8099202	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9675387	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9807157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944715	0.95[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9944767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945783	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs9947206	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9948282	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9949494	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs9951624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952469	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9952654	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956574	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9959813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959905	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9960378	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9963843	0.94[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
rs9963153	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43825400-43844200	Weak transcription	Fetal Brain Female	brain
2	chr18:43826600-43847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:43826800-43843600	Weak transcription	Brain Germinal Matrix	brain
4	chr18:43829200-43840400	Weak transcription	K562	blood
5	chr18:43829200-43842800	Weak transcription	Fetal Muscle Leg	muscle
6	chr18:43830000-43854200	Weak transcription	Esophagus	oesophagus
7	chr18:43830400-43842800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr18:43830600-43847400	Weak transcription	Pancreas	Pancrea
9	chr18:43830800-43842600	Weak transcription	Gastric	stomach
10	chr18:43831000-43840200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr18:43831000-43840200	Weak transcription	Brain Angular Gyrus	brain
12	chr18:43831000-43842800	Weak transcription	Small Intestine	intestine
13	chr18:43831000-43844600	Weak transcription	Spleen	Spleen
14	chr18:43831000-43851400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr18:43831200-43840200	Weak transcription	Stomach Mucosa	stomach
16	chr18:43831200-43842800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr18:43831200-43843000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr18:43831400-43840200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr18:43831400-43840400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr18:43831400-43841000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr18:43831400-43842000	Weak transcription	Fetal Intestine Large	intestine
22	chr18:43831400-43842600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr18:43831400-43842600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr18:43831400-43842800	Weak transcription	Brain Substantia Nigra	brain
25	chr18:43831400-43842800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr18:43831400-43848000	Weak transcription	Fetal Kidney	kidney
27	chr18:43831400-43863200	Weak transcription	Fetal Intestine Small	intestine
28	chr18:43831600-43840200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr18:43831600-43842600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr18:43831600-43842600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr18:43831600-43842800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr18:43831600-43842800	Weak transcription	Hela-S3	cervix
33	chr18:43833400-43843000	Weak transcription	Adipose Nuclei	Adipose
34	chr18:43833600-43842800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr18:43833800-43856800	Weak transcription	Aorta	Aorta
36	chr18:43834400-43841800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:43834600-43842800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr18:43834600-43844000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr18:43834800-43842600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr18:43834800-43842600	Weak transcription	Liver	Liver
41	chr18:43834800-43849000	Weak transcription	HUVEC	blood vessel
42	chr18:43835000-43842800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:43835000-43842800	Weak transcription	HepG2	liver
44	chr18:43835200-43842000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr18:43835200-43842000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr18:43835200-43842800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:43835400-43840200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr18:43835400-43841600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr18:43835400-43842800	Weak transcription	Fetal Lung	lung
50	chr18:43836000-43842600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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