Variant report

Variant	rs4562683
Chromosome Location	chr1:174574726-174574727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 240 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:233)

rs_ID	r²[population]
rs1013769	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10489260	0.85[EUR][1000 genomes]
rs10489264	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494492	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10798314	0.84[EUR][1000 genomes]
rs10798315	0.84[EUR][1000 genomes]
rs10798324	0.84[EUR][1000 genomes]
rs10912789	0.82[EUR][1000 genomes]
rs10912791	0.84[EUR][1000 genomes]
rs10912795	0.86[EUR][1000 genomes]
rs10912806	0.86[EUR][1000 genomes]
rs10912817	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912821	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912822	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912823	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912828	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912829	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484645	0.85[EUR][1000 genomes]
rs11487400	0.84[ASN][1000 genomes]
rs11487401	0.84[ASN][1000 genomes]
rs11799535	0.80[EUR][1000 genomes]
rs11802092	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805578	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806996	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11807229	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11809482	0.88[EUR][1000 genomes]
rs12058377	0.84[EUR][1000 genomes]
rs12062016	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063545	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064403	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12064749	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12065454	0.86[EUR][1000 genomes]
rs12065825	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067463	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12069134	0.83[EUR][1000 genomes]
rs12074416	0.81[EUR][1000 genomes]
rs12076548	0.84[EUR][1000 genomes]
rs12077381	0.81[EUR][1000 genomes]
rs12078960	0.83[EUR][1000 genomes]
rs12079118	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079334	0.84[EUR][1000 genomes]
rs12079757	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12079879	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080407	0.80[EUR][1000 genomes]
rs12080535	0.97[ASN][1000 genomes]
rs12081012	0.88[EUR][1000 genomes]
rs12081046	0.88[EUR][1000 genomes]
rs12082012	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082139	0.97[ASN][1000 genomes]
rs12083628	0.97[ASN][1000 genomes]
rs12083972	0.85[EUR][1000 genomes]
rs12084948	0.88[EUR][1000 genomes]
rs12085652	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093966	0.88[EUR][1000 genomes]
rs12095679	0.88[EUR][1000 genomes]
rs12097931	0.83[EUR][1000 genomes]
rs1329281	0.85[EUR][1000 genomes]
rs1474575	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149099	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1613634	0.81[EUR][1000 genomes]
rs1618207	0.85[EUR][1000 genomes]
rs1622802	0.85[EUR][1000 genomes]
rs1653630	0.85[EUR][1000 genomes]
rs1653634	0.85[EUR][1000 genomes]
rs16846949	0.80[EUR][1000 genomes]
rs16847012	0.83[EUR][1000 genomes]
rs16847335	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16847337	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1754353	0.84[EUR][1000 genomes]
rs1754354	0.83[EUR][1000 genomes]
rs17842156	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17842157	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793292	0.88[EUR][1000 genomes]
rs1793294	0.88[EUR][1000 genomes]
rs1793295	0.86[EUR][1000 genomes]
rs1793298	0.86[EUR][1000 genomes]
rs1793316	0.84[EUR][1000 genomes]
rs1793318	0.83[EUR][1000 genomes]
rs1793320	0.85[EUR][1000 genomes]
rs1813136	0.89[EUR][1000 genomes]
rs1923818	0.87[EUR][1000 genomes]
rs193082	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2060158	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2072759	0.88[EUR][1000 genomes]
rs2092084	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142632	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146564	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163628	0.85[EUR][1000 genomes]
rs2183202	0.85[EUR][1000 genomes]
rs2281009	0.88[EUR][1000 genomes]
rs2281010	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2281011	0.88[EUR][1000 genomes]
rs2568096	0.85[EUR][1000 genomes]
rs2568098	0.86[EUR][1000 genomes]
rs2760057	0.85[EUR][1000 genomes]
rs2760058	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2771401	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2860725	0.83[EUR][1000 genomes]
rs2861003	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861005	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861006	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2901820	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3117838	0.87[EUR][1000 genomes]
rs3117843	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3118990	0.81[EUR][1000 genomes]
rs332763	0.92[ASN][1000 genomes]
rs332764	0.92[ASN][1000 genomes]
rs332767	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332768	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332772	0.92[ASN][1000 genomes]
rs332779	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332781	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332782	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332784	0.83[ASN][1000 genomes]
rs332786	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332793	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332797	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332798	0.82[ASN][1000 genomes]
rs332800	0.87[EUR][1000 genomes]
rs332801	0.87[EUR][1000 genomes]
rs332802	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs332804	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332806	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333422	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333423	0.92[ASN][1000 genomes]
rs333432	0.87[EUR][1000 genomes]
rs333436	0.86[EUR][1000 genomes]
rs333437	0.92[ASN][1000 genomes]
rs333438	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333452	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333453	0.85[ASN][1000 genomes]
rs333454	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs333471	0.92[ASN][1000 genomes]
rs34409674	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36127331	0.81[EUR][1000 genomes]
rs3862941	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920486	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392307	0.86[EUR][1000 genomes]
rs395109	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398350	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs399530	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs411665	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41266050	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4451598	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458242	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs460878	0.86[EUR][1000 genomes]
rs4615901	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464540	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs464635	0.86[EUR][1000 genomes]
rs4651103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651114	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652365	0.80[EUR][1000 genomes]
rs4652460	0.84[EUR][1000 genomes]
rs4652494	0.86[EUR][1000 genomes]
rs4652511	0.88[EUR][1000 genomes]
rs4652512	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4652513	0.88[EUR][1000 genomes]
rs4652652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652669	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652797	0.86[EUR][1000 genomes]
rs467437	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55643907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55667039	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55688014	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55748748	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55844798	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55945681	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56200626	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56260545	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56292878	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56407387	0.80[EUR][1000 genomes]
rs57512497	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60811893	0.87[EUR][1000 genomes]
rs61624206	0.97[ASN][1000 genomes]
rs6656925	0.84[EUR][1000 genomes]
rs6663959	0.86[EUR][1000 genomes]
rs6665535	0.86[EUR][1000 genomes]
rs6667107	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674239	0.84[EUR][1000 genomes]
rs6675515	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6677262	0.83[EUR][1000 genomes]
rs6677874	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682070	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6682997	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6689153	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689327	0.84[EUR][1000 genomes]
rs6689589	0.87[EUR][1000 genomes]
rs6691118	0.97[ASN][1000 genomes]
rs6696465	0.85[EUR][1000 genomes]
rs6696945	0.87[EUR][1000 genomes]
rs6701619	0.86[EUR][1000 genomes]
rs72713583	0.83[EUR][1000 genomes]
rs72713584	0.83[EUR][1000 genomes]
rs72713586	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72713591	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72713602	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72715204	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72715216	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72715218	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72715224	0.88[EUR][1000 genomes]
rs72715226	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72715237	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72715240	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72715245	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715259	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715262	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715273	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715281	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72715292	0.87[EUR][1000 genomes]
rs72715294	0.82[EUR][1000 genomes]
rs72715300	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72717608	0.85[EUR][1000 genomes]
rs72717616	0.85[EUR][1000 genomes]
rs72717617	0.82[EUR][1000 genomes]
rs72717618	0.84[EUR][1000 genomes]
rs74126805	0.83[EUR][1000 genomes]
rs74128393	0.80[EUR][1000 genomes]
rs7413513	0.80[EUR][1000 genomes]
rs7414200	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515116	0.84[EUR][1000 genomes]
rs7516353	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521109	0.85[EUR][1000 genomes]
rs7530265	0.97[ASN][1000 genomes]
rs7537823	0.86[EUR][1000 genomes]
rs7542775	0.97[ASN][1000 genomes]
rs7550472	0.88[EUR][1000 genomes]
rs909533	0.87[EUR][1000 genomes]
rs913688	0.84[EUR][1000 genomes]
rs969472	0.83[EUR][1000 genomes]
rs989424	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3434296	chr1:174556344-174594264	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4562683	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs4562683	RP11-160H22.5	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174555000-174575000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:174566800-174586600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:174568400-174588800	Weak transcription	Esophagus	oesophagus
4	chr1:174570400-174575800	Weak transcription	Gastric	stomach
5	chr1:174572600-174587800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:174572800-174574800	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:174572800-174575000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:174572800-174606200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:174573000-174575000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:174573000-174575600	Weak transcription	Spleen	Spleen
11	chr1:174573000-174587200	Weak transcription	Fetal Intestine Large	intestine
12	chr1:174573200-174574800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:174573200-174581800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:174573200-174589000	Weak transcription	Ovary	ovary
15	chr1:174573400-174575200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:174573400-174577800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:174573400-174584400	Weak transcription	Fetal Stomach	stomach
18	chr1:174573400-174586800	Weak transcription	Pancreas	Pancrea
19	chr1:174573400-174587000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:174573400-174587400	Weak transcription	Primary T cells from cord blood	blood
21	chr1:174573600-174584400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:174574000-174587000	Weak transcription	Primary B cells from cord blood	blood
23	chr1:174574400-174574800	Enhancers	HepG2	liver
24	chr1:174574400-174588800	Weak transcription	Primary B cells from peripheral blood	blood

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