Variant report

Variant	rs9963843
Chromosome Location	chr18:43842618-43842619
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs11082512	0.84[CHB][hapmap]
rs11082514	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11082518	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12457740	0.82[EUR][1000 genomes]
rs12605945	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12607898	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12608232	0.88[EUR][1000 genomes]
rs12709736	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12962307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12962951	0.92[EUR][1000 genomes]
rs12963787	0.92[EUR][1000 genomes]
rs12963943	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12967694	0.84[CHB][hapmap]
rs12969147	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381496	0.82[EUR][1000 genomes]
rs13381515	0.83[EUR][1000 genomes]
rs13381523	0.84[EUR][1000 genomes]
rs13381525	0.84[EUR][1000 genomes]
rs13381529	0.83[EUR][1000 genomes]
rs1791407	0.83[JPT][hapmap]
rs1791413	0.83[JPT][hapmap]
rs1791414	0.83[JPT][hapmap]
rs1808946	0.95[EUR][1000 genomes]
rs36191490	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3744858	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4335852	0.88[EUR][1000 genomes]
rs4453594	0.92[EUR][1000 genomes]
rs4453596	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4542747	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4574015	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4627465	0.83[EUR][1000 genomes]
rs4890317	0.89[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs4890319	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4890320	0.93[EUR][1000 genomes]
rs4890321	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4890626	0.83[EUR][1000 genomes]
rs4890628	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890629	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890631	0.92[EUR][1000 genomes]
rs4890632	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4890633	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4890634	0.92[EUR][1000 genomes]
rs55747741	0.84[EUR][1000 genomes]
rs62096523	0.82[EUR][1000 genomes]
rs62096524	0.83[EUR][1000 genomes]
rs62096525	0.82[EUR][1000 genomes]
rs62096526	0.82[EUR][1000 genomes]
rs62098160	0.87[EUR][1000 genomes]
rs6507676	0.81[EUR][1000 genomes]
rs6507677	0.86[EUR][1000 genomes]
rs6507679	0.83[JPT][hapmap]
rs6507680	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6507681	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6507682	0.88[EUR][1000 genomes]
rs6507690	0.93[EUR][1000 genomes]
rs6507691	0.92[EUR][1000 genomes]
rs6507692	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6507693	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs718513	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs718514	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7227847	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7228365	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7230154	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7230995	0.92[EUR][1000 genomes]
rs7231430	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7231820	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7234695	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7236687	0.82[EUR][1000 genomes]
rs7239351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7240354	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7241527	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7241829	0.81[EUR][1000 genomes]
rs7242375	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7245091	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs73425119	0.83[EUR][1000 genomes]
rs7506126	0.83[JPT][hapmap]
rs8084309	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs8084827	0.83[EUR][1000 genomes]
rs8084829	0.90[EUR][1000 genomes]
rs8085138	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8086610	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8086956	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8090542	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8093407	0.95[EUR][1000 genomes]
rs8094070	0.95[EUR][1000 genomes]
rs8094706	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8095142	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8095729	0.83[EUR][1000 genomes]
rs8095799	0.90[EUR][1000 genomes]
rs8098751	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8099202	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9675387	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs9807157	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs9944715	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9944767	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs9944836	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs9945783	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9947206	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9948282	0.90[EUR][1000 genomes]
rs9949494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9951624	0.95[EUR][1000 genomes]
rs9952469	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9952654	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9956574	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs9959526	0.83[JPT][hapmap]
rs9959813	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9959905	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs9960378	0.93[EUR][1000 genomes]
rs9963153	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9967229	0.83[JPT][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
rs9963843	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr18:43829200-43842800	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:43830000-43854200	Weak transcription	Esophagus	oesophagus
6	chr18:43830400-43842800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr18:43830600-43847400	Weak transcription	Pancreas	Pancrea
8	chr18:43831000-43842800	Weak transcription	Small Intestine	intestine
9	chr18:43831000-43844600	Weak transcription	Spleen	Spleen
10	chr18:43831000-43851400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr18:43831200-43842800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr18:43831200-43843000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr18:43831400-43842800	Weak transcription	Brain Substantia Nigra	brain
14	chr18:43831400-43842800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr18:43831400-43848000	Weak transcription	Fetal Kidney	kidney
16	chr18:43831400-43863200	Weak transcription	Fetal Intestine Small	intestine
17	chr18:43831600-43842800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr18:43831600-43842800	Weak transcription	Hela-S3	cervix
19	chr18:43833400-43843000	Weak transcription	Adipose Nuclei	Adipose
20	chr18:43833600-43842800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr18:43833800-43856800	Weak transcription	Aorta	Aorta
22	chr18:43834600-43842800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr18:43834600-43844000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr18:43834800-43849000	Weak transcription	HUVEC	blood vessel
25	chr18:43835000-43842800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr18:43835000-43842800	Weak transcription	HepG2	liver
27	chr18:43835200-43842800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:43835400-43842800	Weak transcription	Fetal Lung	lung
29	chr18:43836200-43843800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:43837400-43843000	Weak transcription	Brain Hippocampus Middle	brain
31	chr18:43839400-43842800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr18:43839400-43843000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr18:43839400-43843000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr18:43839400-43844600	Enhancers	Psoas Muscle	Psoas
35	chr18:43839600-43842800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr18:43839600-43843200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr18:43839600-43843400	Enhancers	Right Ventricle	heart
38	chr18:43839600-43845000	Enhancers	HMEC	breast
39	chr18:43839600-43845600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr18:43840000-43842800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr18:43840000-43842800	Weak transcription	Lung	lung
42	chr18:43840000-43842800	Weak transcription	Ovary	ovary
43	chr18:43840000-43843200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:43840000-43845000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr18:43840000-43846000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr18:43840000-43846000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr18:43840000-43853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr18:43840200-43844000	Strong transcription	Primary T cells from cord blood	blood
49	chr18:43840600-43843000	Enhancers	NH-A	brain
50	chr18:43840600-43843800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links