Variant report

Variant	rs10028669
Chromosome Location	chr4:120295197-120295198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 201 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:193)

rs_ID	r²[population]
rs10000795	0.81[EUR][1000 genomes]
rs10002914	0.83[EUR][1000 genomes]
rs10003567	0.81[ASN][1000 genomes]
rs10005237	0.81[ASN][1000 genomes]
rs10005973	0.91[ASN][1000 genomes]
rs10006877	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10008386	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008392	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10012456	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10013652	0.82[EUR][1000 genomes]
rs10014719	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10016944	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10017271	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10017371	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10017543	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10020034	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020141	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10020256	0.80[EUR][1000 genomes]
rs1002152	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10021601	0.81[EUR][1000 genomes]
rs10023569	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10024844	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10024933	0.87[ASN][1000 genomes]
rs10025054	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10026436	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10027498	0.81[AMR][1000 genomes]
rs10028423	0.87[AMR][1000 genomes]
rs10031718	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212714	0.86[ASN][1000 genomes]
rs10212719	0.86[ASN][1000 genomes]
rs10212775	0.81[ASN][1000 genomes]
rs10213158	0.87[ASN][1000 genomes]
rs10213267	0.81[ASN][1000 genomes]
rs1022145	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10517834	0.81[EUR][1000 genomes]
rs10518300	0.87[ASN][1000 genomes]
rs10518331	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857068	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11098501	0.87[ASN][1000 genomes]
rs11098502	0.87[ASN][1000 genomes]
rs11098505	0.82[EUR][1000 genomes]
rs11098506	0.81[EUR][1000 genomes]
rs11098512	0.83[AMR][1000 genomes]
rs11098513	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098514	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1112817	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11722183	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11722872	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11723581	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724409	0.87[ASN][1000 genomes]
rs11728730	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729991	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732087	0.81[ASN][1000 genomes]
rs11732686	0.87[ASN][1000 genomes]
rs11737400	0.83[ASN][1000 genomes]
rs12374244	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12374245	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12374352	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12498994	0.87[ASN][1000 genomes]
rs12499602	0.80[EUR][1000 genomes]
rs12501602	0.82[EUR][1000 genomes]
rs12504149	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12505469	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12506148	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12506610	0.81[ASN][1000 genomes]
rs12507565	0.87[ASN][1000 genomes]
rs12508173	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12509234	0.86[AMR][1000 genomes]
rs12509621	0.87[ASN][1000 genomes]
rs12510269	0.81[ASN][1000 genomes]
rs12510451	0.83[EUR][1000 genomes]
rs12510487	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12511640	0.87[ASN][1000 genomes]
rs12512118	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512154	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12513083	0.87[ASN][1000 genomes]
rs12513310	0.82[EUR][1000 genomes]
rs12711071	0.81[ASN][1000 genomes]
rs13104396	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13105020	0.82[EUR][1000 genomes]
rs13108589	0.94[ASN][1000 genomes]
rs13125526	0.82[EUR][1000 genomes]
rs13132082	0.82[EUR][1000 genomes]
rs13133522	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13149954	0.83[ASN][1000 genomes]
rs13151285	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1511017	0.87[ASN][1000 genomes]
rs1511025	0.81[ASN][1000 genomes]
rs1546502	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1546504	0.87[AMR][1000 genomes]
rs1546505	0.88[AMR][1000 genomes]
rs17049949	0.87[ASN][1000 genomes]
rs17595608	0.87[ASN][1000 genomes]
rs1980024	0.87[ASN][1000 genomes]
rs1980025	0.87[ASN][1000 genomes]
rs1980026	0.87[ASN][1000 genomes]
rs1980027	0.87[ASN][1000 genomes]
rs2002049	0.83[ASN][1000 genomes]
rs2017057	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2036856	0.87[ASN][1000 genomes]
rs2036857	0.87[ASN][1000 genomes]
rs2036860	0.87[ASN][1000 genomes]
rs2389802	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28363929	0.87[ASN][1000 genomes]
rs28373117	0.87[ASN][1000 genomes]
rs28403131	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28491261	0.87[AMR][1000 genomes]
rs28501434	0.81[EUR][1000 genomes]
rs28549914	0.84[EUR][1000 genomes]
rs28572238	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28580295	0.83[ASN][1000 genomes]
rs28633994	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28643450	0.84[ASN][1000 genomes]
rs28652763	0.81[ASN][1000 genomes]
rs28668103	0.81[EUR][1000 genomes]
rs28713555	0.87[ASN][1000 genomes]
rs28714195	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28857482	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964	0.81[ASN][1000 genomes]
rs34425882	0.86[ASN][1000 genomes]
rs34685788	0.81[ASN][1000 genomes]
rs34913743	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35091806	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35165976	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3864141	0.94[ASN][1000 genomes]
rs3890049	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3955380	0.80[AMR][1000 genomes]
rs4079144	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4107728	0.87[ASN][1000 genomes]
rs4296662	0.80[AMR][1000 genomes]
rs4309825	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4345162	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4443261	0.87[ASN][1000 genomes]
rs4463052	0.90[AMR][1000 genomes]
rs4472123	0.81[ASN][1000 genomes]
rs4560394	0.81[AMR][1000 genomes]
rs4604043	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59394118	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59866101	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62320740	0.83[ASN][1000 genomes]
rs66900435	0.87[ASN][1000 genomes]
rs6820376	0.81[ASN][1000 genomes]
rs6824111	0.81[EUR][1000 genomes]
rs6824169	0.82[EUR][1000 genomes]
rs6832410	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6838236	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6838617	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845714	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846442	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846620	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847075	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847248	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6847586	0.81[EUR][1000 genomes]
rs6847778	0.83[EUR][1000 genomes]
rs6848580	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857105	0.83[AMR][1000 genomes]
rs6857892	0.81[EUR][1000 genomes]
rs714899	0.81[ASN][1000 genomes]
rs71610279	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs71610280	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72676045	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72676046	0.87[ASN][1000 genomes]
rs7437420	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7654700	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7672129	0.86[ASN][1000 genomes]
rs7672372	0.85[ASN][1000 genomes]
rs7672493	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7672594	0.87[ASN][1000 genomes]
rs7672778	0.87[ASN][1000 genomes]
rs7673476	0.87[ASN][1000 genomes]
rs7677068	0.81[EUR][1000 genomes]
rs7689729	0.87[ASN][1000 genomes]
rs7695996	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7696465	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7696649	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7696857	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7696875	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878372	0.81[ASN][1000 genomes]
rs878373	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs878376	0.81[ASN][1000 genomes]
rs907204	0.81[ASN][1000 genomes]
rs907205	0.81[ASN][1000 genomes]
rs9991166	0.81[ASN][1000 genomes]
rs9991221	0.83[EUR][1000 genomes]
rs9991959	0.87[ASN][1000 genomes]
rs9993347	0.88[ASN][1000 genomes]
rs9995045	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995136	0.81[EUR][1000 genomes]
rs9995234	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995244	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9996417	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9998953	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9999724	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10028669	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs10028669	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs10028669	RP11-33B1.1	cis	Stomach	GTEx
rs10028669	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs10028669	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs10028669	RP11-33B1.4	cis	Whole Blood	GTEx
rs10028669	RP11-33B1.1	cis	Thyroid	GTEx
rs10028669	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs10028669	RP11-33B1.1	cis	lung	GTEx
rs10028669	RP11-33B1.1	cis	Whole Blood	GTEx
rs10028669	RP11-384K6.6	cis	Whole Blood	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120292200-120295400	Weak transcription	Thymus	Thymus
2	chr4:120292600-120295600	Enhancers	Primary T cells from cord blood	blood
3	chr4:120293800-120296000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr4:120293800-120296800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:120294000-120295400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:120294000-120295800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:120294400-120295800	Weak transcription	Fetal Thymus	thymus
8	chr4:120294600-120297000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr4:120295000-120295400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:120295000-120295800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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