PiER - Linking variants to core genes

BOOKLET

eV2CG - Linking to core genes from input SNPs

Error Message: your input at Step 1

Please check your input SNP identifiers (dbSNP rsIDs) and p-values (between 0 and 1); otherwise they will be ignored.
Please paste your own data at Step 1 every time before clicking the Submit button. Notably, the text box at Step 1 is always pre-filled with the provided example when the interface page is first-visited or refreshed.

eV2CG - Linking ... (please don't refresh this page)

Show Info Example I/O

Input

(Step 1) a list of user-input SNPs, with 1st column for dbSNP rsIDs and 2nd column for significance info (p-values between 0 and 1). The error message will be displayed if the input is invalid. Example Input, shared genetic variants identified from cross-disease genome-wide association studies in inflammatory disorders (Nature Genetics 2016; PMID26974007).

Mechanism

(Step 2) includes SNPs in Linkage Disequilibrium (LD). By default, input SNPs with a typical threshold (p-value < 5e−8) are considered, and additional SNPs in linkage disequilibrium (R2 < 0.8) can be also included according to the European population.
(Step 3) uses genomic proximity, quantitative trait locus (QTL), or promoter capture Hi-C (PCHi-C) to identify core genes.
(More Controls) fine-tunes parameters involved in steps described above.

Output

( Example Output) includes two interactive tables for core genes and evidence used, and a manhattan plot (illustrating scored core genes color-coded by chromosomes). A summary of input data and the runtime (computed on the server side) is also returned to the users for the reference.

Other useful information

At step 1, first prepare the tab-delimited input using Microsoft Excel and then do copying/pasting (the text box is pre-filled with the provided example).
Since the text box at Step 1 is always pre-filled with the provided example when the interface page is first-visited or refreshed, it is very important to paste your own data every time before clicking the Submit button.
Currently only one run is allowed for the same machine and the same browser (concurrent client instances are not supported).
Precaution should be taken when applying to disease areas where e/pQTL and PCHi-C datasets are not directly relevant.
Precaution should be also taken using the default parameters empirically optimised for immune-mediated diseases. The users are advised to try different values and decide on the optimal ones, if available, also considering other relevant information for disease under study.
Please drop for bug reports and enquires.

Step 1: Paste your SNPs here (1st column for dbSNP rsIDs, 2nd for significance info).

snp	pvalue
rs11190133	0.000000006
rs10743181	0.00000002
rs11229555	0.00000004
rs11230563	5E-15
rs174535	2E-11
rs559928	8E-14
rs568617	0.00000004
rs11236797	3E-43
rs7115956	8E-12
rs4561177	0.000000001
rs661054	2E-14
rs7933433	1E-10
rs11221332	2E-10
rs1860545	3E-17
rs11616188	3E-14
rs7313895	4E-17
rs11168249	0.000000006
rs11614178	2E-34
rs12369214	0.00000002
rs3184504	4E-10
rs17085007	2E-13
rs941823	7E-11
rs6561151	1E-22
rs6651252	2E-17
rs10758669	5E-43
rs2812378	0.000000006
rs7848647	1E-25
rs726657	1E-14
rs7468800	0.000000002
rs4986790	0.00000001
rs10870077	6E-45
rs141992399	1E-31
rs3124998	9E-09
rs61839660	1E-15
rs3118471	4E-13
rs76913543	4E-12
rs2104286	0.00000004
rs2236379	9E-09
rs2050392	0.000000002
rs34779708	5E-29
rs10995271	3E-48
rs7915475	3E-10
rs2227551	0.00000003
rs1250573	2E-22
rs7097656	1E-13
rs1800682	0.000000004
rs2497318	3E-11
rs10748781	6E-51
rs1847472	5E-10
rs4946717	1E-21
rs28701841	6E-10
rs9491891	5E-15
rs582757	1E-16
rs928722	4E-14
rs9494840	0.000000003
rs2451258	5E-17
rs67025039	9E-25
rs1182188	4E-11
rs1525735	9E-09
rs28550029	3E-18
rs860262	0.000000007
rs4917129	4E-12
rs12718244	0.000000002
rs9297145	0.00000001
rs6466198	1E-21
rs7805114	5E-11
rs4728142	2E-11
rs2538470	2E-10
rs10094579	2E-10
rs1551399	4E-19
rs2042011	0.00000004
rs11749040	7E-28
rs9687958	3E-16
rs353339	5E-13
rs71624119	0.00000002
rs4703855	0.00000003
rs34804116	3E-10
rs469758	6E-54
rs2910686	2E-21
rs2549803	4E-12
rs17622378	2E-55
rs6863411	0.000000002
rs11749391	2E-42
rs74817271	2E-26
rs56167332	3E-43
rs12188300	3E-34
rs4921482	9E-25
rs6556411	3E-11
rs72812861	0.00000001
rs1267499	1E-11
rs2328530	1E-17
rs714830	0.000000005
rs71559680	6E-12
rs72928038	2E-10
rs16841904	0.000000002
rs7552167	0.00000001
rs12131796	5E-41
rs3024493	1E-38
rs12075255	3E-11
rs2666218	9E-10
rs13407913	3E-18
rs6600247	9E-29
rs80174646	1E-143
rs7517847	1E-98
rs10889676	2E-24
rs183686347	6E-14
rs2476601	3E-12
rs4845604	2E-16
rs6693105	4E-24
rs11675538	0.00000003
rs4851529	1E-14
rs12987977	3E-17
rs871656	0.000000001
rs2111485	3E-13
rs35667974	5E-10
rs3747517	0.000000002
rs72871627	0.00000001
rs17229679	3E-17
rs6434978	1E-10
rs34920465	3E-13
rs2816958	4E-15
rs6697886	2E-10
rs2234161	2E-11
rs3766606	9E-14
rs6426833	7E-62
rs3806308	1E-24
rs4655215	8E-20
rs1260326	2E-23
rs925255	8E-18
rs77981966	2E-16
rs7608910	2E-32
rs702872	4E-11
rs4672505	2E-52
rs4129267	9E-18
rs4971079	3E-10
rs78973538	0.00000003
rs1333062	2E-11
rs10800314	1E-32
rs61802846	0.000000001
rs6425143	1E-17
rs4243971	0.000000005
rs6058869	0.000000004
rs4812833	7E-16
rs1883832	4E-12
rs1328454	0.000000004
rs259964	4E-12
rs6062496	2E-30
rs2823288	4E-28
rs2284553	4E-16
rs9977672	5E-54
rs1893592	0.000000006
rs4456788	6E-25
rs2266961	4E-15
rs140135	0.000000006
rs2143178	2E-33
rs5757584	0.000000004
rs1569414	6E-10
rs10761648	6E-16
rs10775412	3E-19
rs28998802	7E-12
rs9797244	1E-10
rs9889296	5E-21
rs35736272	6E-30
rs12942547	2E-15
rs12943464	2E-14
rs3853824	0.00000002
rs1292035	3E-11
rs196941	8E-10
rs17780256	6E-11
rs66504140	0.00000002
rs12968719	2E-26
rs62097857	1E-11
rs2024092	2E-18
rs72977586	0.000000004
rs74956615	2E-22
rs35018800	5E-12
rs12720356	0.000000002
rs35074907	0.000000006
rs4802307	2E-11
rs679574	1E-17
rs9554587	9E-10
rs2145623	3E-10
rs8006884	7E-10
rs1569328	0.000000002
rs11624293	2E-17
rs16967103	0.000000005
rs17293632	1E-16
rs35874463	1E-11
rs367569	5E-14
rs11649613	3E-10
rs7195296	3E-13
rs7404095	0.000000003
rs26528	3E-29
rs11363316	4E-30
rs11574938	5E-14
rs1870293	1E-10
rs2066845	6E-94
rs2357623	4E-48
rs72796367	1E-16
rs2066847	0
rs11117431	5E-16
rs12932970	0.00000001
rs7426056	1E-20
rs5837881	3E-12
rs11676348	2E-11
rs7556897	8E-12
rs12694846	5E-15
rs35300242	5E-67
rs3749171	2E-25
rs4676406	6E-10
rs35320439	7E-10
rs73178598	3E-13
rs1001007	0.00000002
rs3197999	7E-55
rs116046827	8E-11
rs6781808	0.000000008
rs11098964	0.00000002
rs13107612	3E-10
rs3774937	2E-18
rs59867199	7E-20
rs11750385	0.00000004
rs3776414	0.000000006
rs395157	8E-15
rs1992661	1E-74

Step 2: Include SNPs in Linkage Disequilibrium (LD) defined by which population.

Population

Step 3: Define core genes based on genomic proximity, quantitative trait locus (QTL) or promoter capture Hi-C (PCHi-C).

Core genes supported by:

SNP significance (SNPs with intolerable significance will be ignored).

P-value threshold:

Manhattan plot (top scored genes to be labelled).

Number of genes: