Variant report

Variant	rs2460254
Chromosome Location	chr11:71570110-71570111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10736781	0.83[EUR][1000 genomes]
rs10751189	0.81[EUR][1000 genomes]
rs12291678	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1612492	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1629046	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1629722	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1783959	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1783960	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783961	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783962	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1791449	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1791450	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1791451	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1791452	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939248	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186637	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2363736	0.81[EUR][1000 genomes]
rs2460252	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460253	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508578	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2511097	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511098	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511099	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2845856	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2885880	0.81[EUR][1000 genomes]
rs2945921	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2945922	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3016288	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3016289	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3016291	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34390540	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886589	0.83[EUR][1000 genomes]
rs4121395	0.83[EUR][1000 genomes]
rs4479013	0.83[EUR][1000 genomes]
rs474231	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs475759	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475959	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs479487	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs481300	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs481355	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs482413	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488799	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944232	0.88[EUR][1000 genomes]
rs4944242	0.83[EUR][1000 genomes]
rs4945340	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945353	0.83[EUR][1000 genomes]
rs497867	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499386	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506395	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs507216	0.88[ASN][1000 genomes]
rs508230	0.87[ASN][1000 genomes]
rs513292	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs514431	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs515358	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs518830	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519098	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520025	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528942	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529522	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs529567	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs531326	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532433	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs548127	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs550230	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556089	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs558859	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55972015	0.88[EUR][1000 genomes]
rs560626	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs562414	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs562469	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562621	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs564170	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566965	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573137	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573227	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs579254	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59339387	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596130	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs596629	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599611	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs601865	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs603680	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604671	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607319	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609181	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609492	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs613140	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613535	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613971	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618186	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629714	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633448	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634829	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs635442	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs635701	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636184	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs650542	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654780	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657819	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658661	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658699	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592448	0.83[EUR][1000 genomes]
rs6592449	0.83[EUR][1000 genomes]
rs6592450	0.81[EUR][1000 genomes]
rs6592451	0.83[EUR][1000 genomes]
rs661242	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs662649	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs669835	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671072	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671394	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs672424	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs672533	0.82[EUR][1000 genomes]
rs674688	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs674735	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs675156	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680150	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs686205	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692940	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693648	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102192	0.88[EUR][1000 genomes]
rs7103210	0.88[EUR][1000 genomes]
rs7106748	0.88[EUR][1000 genomes]
rs7924516	0.83[EUR][1000 genomes]
rs7926533	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7943227	0.81[EUR][1000 genomes]
rs7944073	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7948821	0.88[EUR][1000 genomes]
rs947932	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	esv3527986	chr11:71298409-71620955	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv3527987	chr11:71298409-71620955	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv2761682	chr11:71299175-71619923	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv897904	chr11:71316093-71615727	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv972041	chr11:71330518-71615123	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv3369013	chr11:71338874-71612242	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv2758276	chr11:71363639-71657576	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	esv2759836	chr11:71363639-71657576	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv428262	chr11:71363639-71804055	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
11	nsv897905	chr11:71371354-71615727	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv1819073	chr11:71371742-71618164	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	esv11824	chr11:71515433-71603968	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv18828	chr11:71551614-71592576	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2460254	NUMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71565800-71575000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:71566800-71570800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:71569400-71575600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:71570000-71570600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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