Variant report

Variant	rs2861006
Chromosome Location	chr1:174681071-174681072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 233 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:229)

rs_ID	r²[population]
rs1012182	0.82[EUR][1000 genomes]
rs10489264	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10494492	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10798324	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798327	0.84[EUR][1000 genomes]
rs10912817	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912821	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912822	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912823	0.92[ASN][1000 genomes]
rs10912828	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912829	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912843	0.85[EUR][1000 genomes]
rs10912853	0.81[EUR][1000 genomes]
rs10912855	0.82[EUR][1000 genomes]
rs11800350	0.87[EUR][1000 genomes]
rs11802092	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11805578	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11806996	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11809803	0.85[EUR][1000 genomes]
rs11810508	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12062016	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063093	0.83[EUR][1000 genomes]
rs12063545	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12064403	0.86[ASN][1000 genomes]
rs12064749	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12065825	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12067463	0.92[ASN][1000 genomes]
rs12078839	0.85[EUR][1000 genomes]
rs12079118	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12079757	0.87[ASN][1000 genomes]
rs12079879	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12080535	0.92[ASN][1000 genomes]
rs12082012	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12082139	0.92[ASN][1000 genomes]
rs12083628	0.92[ASN][1000 genomes]
rs12085652	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094876	0.82[EUR][1000 genomes]
rs1231826	0.85[EUR][1000 genomes]
rs1231827	0.85[EUR][1000 genomes]
rs1329281	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474575	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149099	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540207	0.81[EUR][1000 genomes]
rs1613634	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618207	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618408	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1622802	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162815	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1653630	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1653634	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16847335	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847337	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302033	0.85[EUR][1000 genomes]
rs1754352	0.85[EUR][1000 genomes]
rs1754353	0.92[EUR][1000 genomes]
rs1754354	0.92[EUR][1000 genomes]
rs1754360	0.82[ASN][1000 genomes]
rs17842156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17842157	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793292	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793294	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793295	0.95[EUR][1000 genomes]
rs1793298	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793305	0.85[EUR][1000 genomes]
rs1793307	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1793310	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1793316	0.92[EUR][1000 genomes]
rs1793318	0.92[EUR][1000 genomes]
rs1793320	0.94[EUR][1000 genomes]
rs1813136	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1883139	0.86[EUR][1000 genomes]
rs1894201	0.85[EUR][1000 genomes]
rs1923818	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193082	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2003378	0.82[EUR][1000 genomes]
rs2060158	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092084	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2142632	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2146564	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163628	0.94[EUR][1000 genomes]
rs2183202	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2281010	0.81[EUR][1000 genomes]
rs2568096	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568098	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2760057	0.97[EUR][1000 genomes]
rs2760058	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2771401	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860725	0.91[EUR][1000 genomes]
rs2861003	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981893	0.86[EUR][1000 genomes]
rs2981896	0.85[EUR][1000 genomes]
rs2987872	0.85[EUR][1000 genomes]
rs2987873	0.84[EUR][1000 genomes]
rs2987875	0.86[EUR][1000 genomes]
rs2987876	0.84[EUR][1000 genomes]
rs2987880	0.84[EUR][1000 genomes]
rs3117838	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3117843	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3118982	0.86[EUR][1000 genomes]
rs3118986	0.84[EUR][1000 genomes]
rs3118987	0.84[EUR][1000 genomes]
rs3118990	0.89[EUR][1000 genomes]
rs332763	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332764	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332767	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332768	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332772	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332776	0.86[EUR][1000 genomes]
rs332779	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332781	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332782	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332784	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs332786	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332787	0.87[EUR][1000 genomes]
rs332793	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332797	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332798	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs332800	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332801	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332802	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs332804	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs332806	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333422	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333423	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333432	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333436	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333437	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333438	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333452	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333453	0.90[ASN][1000 genomes]
rs333454	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333471	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34409674	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36127331	0.89[EUR][1000 genomes]
rs3862941	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920486	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs392307	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs395109	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398350	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399530	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411665	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266050	0.81[EUR][1000 genomes]
rs4451598	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4480415	0.83[EUR][1000 genomes]
rs4562683	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs458242	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459078	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs460878	0.97[EUR][1000 genomes]
rs4615901	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs464540	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464635	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651103	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651114	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651235	0.81[EUR][1000 genomes]
rs4652512	0.81[EUR][1000 genomes]
rs4652652	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652669	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652797	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467437	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55643907	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55667039	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55688014	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748748	0.81[EUR][1000 genomes]
rs55793234	0.83[EUR][1000 genomes]
rs55844798	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55945681	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56260545	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57289077	0.86[EUR][1000 genomes]
rs60811893	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61624206	0.92[ASN][1000 genomes]
rs6425298	0.86[EUR][1000 genomes]
rs6425300	0.86[EUR][1000 genomes]
rs6425301	0.86[EUR][1000 genomes]
rs6667107	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671196	0.83[EUR][1000 genomes]
rs6671272	0.80[EUR][1000 genomes]
rs6671782	0.82[EUR][1000 genomes]
rs6675515	0.86[ASN][1000 genomes]
rs6677874	0.92[ASN][1000 genomes]
rs66836419	0.85[EUR][1000 genomes]
rs6684229	0.82[EUR][1000 genomes]
rs6684515	0.82[EUR][1000 genomes]
rs6686872	0.82[EUR][1000 genomes]
rs6687616	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6689153	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6690754	0.86[EUR][1000 genomes]
rs6691118	0.92[ASN][1000 genomes]
rs6693979	0.86[EUR][1000 genomes]
rs6696465	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67133776	0.81[EUR][1000 genomes]
rs67203477	0.85[EUR][1000 genomes]
rs67903803	0.85[EUR][1000 genomes]
rs72715218	0.81[EUR][1000 genomes]
rs72715226	0.81[EUR][1000 genomes]
rs72715240	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715245	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715253	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715255	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715259	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715260	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715262	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715273	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715281	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72715292	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715294	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715300	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717608	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717616	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717617	0.90[EUR][1000 genomes]
rs72717618	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72717630	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72717649	0.85[EUR][1000 genomes]
rs72717650	0.85[EUR][1000 genomes]
rs72717653	0.85[EUR][1000 genomes]
rs72717661	0.83[EUR][1000 genomes]
rs7414200	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516353	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516410	0.85[EUR][1000 genomes]
rs7521109	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7530265	0.92[ASN][1000 genomes]
rs7542775	0.92[ASN][1000 genomes]
rs7543147	0.82[EUR][1000 genomes]
rs7547658	0.86[EUR][1000 genomes]
rs913686	0.84[EUR][1000 genomes]
rs913687	0.82[ASN][1000 genomes]
rs913688	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425787	0.86[EUR][1000 genomes]
rs989424	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2861006	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs2861006	RP11-160H22.5	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174665800-174682600	Weak transcription	Left Ventricle	heart
2	chr1:174668400-174682600	Weak transcription	Gastric	stomach
3	chr1:174669600-174684000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:174672600-174682600	Weak transcription	Right Ventricle	heart
5	chr1:174678200-174689000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:174678200-174689200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:174678200-174708600	Weak transcription	Primary T cells from cord blood	blood
8	chr1:174678600-174682600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:174678600-174684400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:174678600-174706400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:174678800-174681400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:174679200-174687000	Weak transcription	Primary B cells from cord blood	blood
13	chr1:174680000-174681200	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr1:174681000-174682000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:174681000-174682800	Strong transcription	Fetal Intestine Small	intestine
16	chr1:174681000-174683600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:174681000-174684000	Weak transcription	Pancreas	Pancrea
18	chr1:174681000-174685400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:174681000-174686200	Weak transcription	Lung	lung

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