Variant report

Variant	rs12509621
Chromosome Location	chr4:120249660-120249661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120249451..120251294-chr4:120987361..120988915,2	K562	blood:

Variant related genes	Relation type
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 184 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs10000544	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10003567	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10005237	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10005973	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10006192	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10006877	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10012408	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10012456	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10016241	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10017271	0.81[ASN][1000 genomes]
rs10017371	0.87[ASN][1000 genomes]
rs10020034	0.85[ASN][1000 genomes]
rs1002152	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10022448	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10023569	0.81[ASN][1000 genomes]
rs10023641	0.89[AFR][1000 genomes]
rs10024844	0.84[ASN][1000 genomes]
rs10024933	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025054	0.84[ASN][1000 genomes]
rs10025925	0.88[AFR][1000 genomes]
rs10026436	0.87[ASN][1000 genomes]
rs10028669	0.87[ASN][1000 genomes]
rs10028773	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10031718	0.85[ASN][1000 genomes]
rs1011054	0.81[EUR][1000 genomes]
rs10212714	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212719	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212775	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10212956	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10213158	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213267	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1022145	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518300	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518331	0.80[ASN][1000 genomes]
rs11098501	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098502	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098513	0.83[ASN][1000 genomes]
rs11722183	0.85[ASN][1000 genomes]
rs11722872	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723581	0.81[ASN][1000 genomes]
rs11724409	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724758	0.80[ASN][1000 genomes]
rs11726229	0.81[EUR][1000 genomes]
rs11728730	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11729991	0.87[ASN][1000 genomes]
rs11732087	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732686	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502393	0.88[AFR][1000 genomes]
rs12502524	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12503171	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12505469	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12506445	0.88[AFR][1000 genomes]
rs12506487	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12506610	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12507565	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510133	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12510269	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12511640	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512118	0.85[ASN][1000 genomes]
rs12512154	0.83[ASN][1000 genomes]
rs12513083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711071	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13104396	0.87[ASN][1000 genomes]
rs13108589	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13116504	0.81[EUR][1000 genomes]
rs13133044	0.81[EUR][1000 genomes]
rs13151285	0.83[ASN][1000 genomes]
rs1511017	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511025	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1546502	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1546503	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1546504	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1546505	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1546506	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17049949	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595608	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814813	0.89[AFR][1000 genomes]
rs1814814	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1980024	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980025	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980026	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980027	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002047	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002049	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017057	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2036856	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036857	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036858	0.85[ASN][1000 genomes]
rs2036860	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136911	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28363929	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369503	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28369518	0.89[AFR][1000 genomes]
rs28373117	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28396837	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28403131	0.87[ASN][1000 genomes]
rs28419773	0.81[EUR][1000 genomes]
rs28437684	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs28502463	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28546691	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28555550	0.81[EUR][1000 genomes]
rs28572238	0.81[ASN][1000 genomes]
rs28589345	0.80[AFR][1000 genomes]
rs28599836	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28633994	0.89[ASN][1000 genomes]
rs28643450	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28652763	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28691602	0.82[AFR][1000 genomes]
rs28713555	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28714087	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28714195	0.81[ASN][1000 genomes]
rs28726222	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2964	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34425882	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34685788	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34818745	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3749591	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3864141	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3864142	0.85[AFR][1000 genomes]
rs3864144	0.87[AFR][1000 genomes]
rs3956464	0.83[AFR][1000 genomes]
rs4107728	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309825	0.83[ASN][1000 genomes]
rs4345162	0.83[ASN][1000 genomes]
rs4422403	0.93[AFR][1000 genomes]
rs4443261	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472123	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4604043	0.83[ASN][1000 genomes]
rs55820750	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs59394118	0.87[ASN][1000 genomes]
rs66900435	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815291	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6838009	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6838236	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6838617	0.85[ASN][1000 genomes]
rs6847075	0.86[ASN][1000 genomes]
rs6847248	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848580	0.86[ASN][1000 genomes]
rs6857105	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs714899	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71591558	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72676045	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72676046	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7437420	0.83[ASN][1000 genomes]
rs7659194	0.81[EUR][1000 genomes]
rs7671759	0.81[AMR][1000 genomes]
rs7671978	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7672129	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672372	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7672493	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672594	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672778	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673476	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689729	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690338	0.82[AMR][1000 genomes]
rs7695996	0.80[ASN][1000 genomes]
rs7696465	0.80[ASN][1000 genomes]
rs7696649	0.80[ASN][1000 genomes]
rs7696857	0.80[ASN][1000 genomes]
rs7696875	0.80[ASN][1000 genomes]
rs878372	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878373	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878376	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907204	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907205	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs938056	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9991166	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9991959	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993347	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995045	0.80[ASN][1000 genomes]
rs9995234	0.80[ASN][1000 genomes]
rs9995716	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9996494	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9996644	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9998953	0.86[ASN][1000 genomes]
rs9999724	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	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	nsv879840	chr4:120227419-120257417	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12509621	RP11-33B1.1	cis	lung	GTEx
rs12509621	RP11-384K6.6	cis	Whole Blood	GTEx
rs12509621	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs12509621	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs12509621	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs12509621	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12509621	RP11-33B1.1	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:120235600-120251000	Weak transcription	Left Ventricle	heart
3	chr4:120244400-120249800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:120249600-120250000	Enhancers	Fetal Intestine Large	intestine
5	chr4:120249600-120250200	Enhancers	Fetal Intestine Small	intestine

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