Variant report

Variant	rs12540013
Chromosome Location	chr7:110677396-110677397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1008413	0.82[EUR][1000 genomes]
rs10225614	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10246351	0.81[EUR][1000 genomes]
rs10260255	0.81[EUR][1000 genomes]
rs10464508	0.93[EUR][1000 genomes]
rs10464637	0.93[EUR][1000 genomes]
rs115826	0.92[EUR][1000 genomes]
rs12534893	0.94[EUR][1000 genomes]
rs12535802	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12540274	0.95[EUR][1000 genomes]
rs12672824	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs166308	0.93[EUR][1000 genomes]
rs174074	0.92[EUR][1000 genomes]
rs17438711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17527832	0.94[EUR][1000 genomes]
rs17528429	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17528930	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2041531	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109863	0.81[EUR][1000 genomes]
rs2191926	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2396300	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258989	0.90[EUR][1000 genomes]
rs258990	0.91[EUR][1000 genomes]
rs258991	0.92[EUR][1000 genomes]
rs258997	0.92[EUR][1000 genomes]
rs258998	0.80[EUR][1000 genomes]
rs258999	0.92[EUR][1000 genomes]
rs259000	0.93[EUR][1000 genomes]
rs259002	0.93[EUR][1000 genomes]
rs259003	0.93[EUR][1000 genomes]
rs259004	0.92[EUR][1000 genomes]
rs259006	0.93[EUR][1000 genomes]
rs259008	0.93[EUR][1000 genomes]
rs259009	0.93[EUR][1000 genomes]
rs259011	0.93[EUR][1000 genomes]
rs259013	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs259015	0.93[EUR][1000 genomes]
rs259017	0.93[EUR][1000 genomes]
rs259018	0.91[EUR][1000 genomes]
rs259020	0.93[EUR][1000 genomes]
rs259021	0.93[EUR][1000 genomes]
rs259022	0.93[EUR][1000 genomes]
rs4141112	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4727753	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4730467	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4730470	0.81[EUR][1000 genomes]
rs4730472	0.82[EUR][1000 genomes]
rs55693011	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56148096	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56160040	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56277540	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56379568	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56907799	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57238777	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58495202	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58585976	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59086405	0.94[EUR][1000 genomes]
rs60581416	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60807734	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6466365	0.80[EUR][1000 genomes]
rs6466366	0.80[EUR][1000 genomes]
rs6466368	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466370	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66596422	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67679818	0.99[EUR][1000 genomes]
rs67759016	0.94[EUR][1000 genomes]
rs67798998	0.92[EUR][1000 genomes]
rs6955060	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6960818	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6972608	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6978507	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs725272	0.92[EUR][1000 genomes]
rs73435146	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs758952	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs758954	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7782551	0.82[EUR][1000 genomes]
rs7795011	0.81[EUR][1000 genomes]
rs7796806	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs876396	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs917763	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9690080	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023596	chr7:109984459-110708071	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539061	chr7:109984459-110708071	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv531434	chr7:110310931-110839892	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3506497	chr7:110484691-111091738	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3506498	chr7:110484750-111091689	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv888973	chr7:110509579-110699652	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv2758129	chr7:110523298-110787849	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2759554	chr7:110523298-110787849	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1031546	chr7:110549137-110978256	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv817555	chr7:110564801-110990927	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1033286	chr7:110588021-110990928	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv539063	chr7:110588021-110990928	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv931978	chr7:110607590-111092490	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1025987	chr7:110609568-111258501	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv888975	chr7:110613685-110677656	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2830178	chr7:110645431-110778571	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1024477	chr7:110660006-110944477	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540013	IMMP2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110670200-110678000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:110671600-110681600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:110672800-110683400	Weak transcription	HepG2	liver
4	chr7:110675800-110681000	Weak transcription	Primary T cells from cord blood	blood

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