Variant report

Variant	rs12554847
Chromosome Location	chr9:10107399-10107400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10511533	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12551049	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12552479	0.83[MEX][hapmap]
rs12552628	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12552905	0.83[MEX][hapmap]
rs12553705	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12554153	1.00[CEU][hapmap]
rs16931013	1.00[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs16931018	1.00[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs16931082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16931103	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17681526	0.97[EUR][1000 genomes]
rs291318	0.85[CEU][hapmap]
rs4741008	1.00[EUR][1000 genomes]
rs4741009	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4741011	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4741012	0.83[MEX][hapmap]
rs55637129	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55737705	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56051561	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56266784	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56283869	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56322487	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59474508	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60210913	0.84[AFR][1000 genomes]
rs60541640	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694816	0.83[EUR][1000 genomes]
rs72694817	0.91[EUR][1000 genomes]
rs72694835	1.00[EUR][1000 genomes]
rs72694837	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72694841	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72694842	1.00[EUR][1000 genomes]
rs72694844	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72694861	1.00[EUR][1000 genomes]
rs72694862	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694863	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694865	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694868	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72694869	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694870	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694871	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694872	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694873	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694879	1.00[EUR][1000 genomes]
rs72694880	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694881	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694882	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694883	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694884	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694888	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694889	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72694890	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72694891	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72694892	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72694893	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72694895	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72694898	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9298651	1.00[CEU][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034731	chr9:9776126-10481262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv892295	chr9:9832245-10380406	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1021380	chr9:9943339-10126281	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv539989	chr9:9943339-10126281	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892301	chr9:9971050-10144584	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv892302	chr9:9974221-10158866	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1030657	chr9:10002355-10481262	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv831506	chr9:10040172-10204609	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv824850	chr9:10058091-10134157	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv892304	chr9:10061872-10119157	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv892305	chr9:10061872-10123735	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv892306	chr9:10077180-10127876	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv471279	chr9:10081386-10115338	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
14	nsv466156	chr9:10081387-10115338	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
15	nsv613373	chr9:10081387-10115338	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv892307	chr9:10081387-10123735	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
17	nsv1021508	chr9:10101315-10131581	Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv973448	chr9:10101449-10109431	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
19	nsv1024401	chr9:10105656-10218577	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv539995	chr9:10105656-10218577	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12554847	SERPINB1	trans	lymphoblastoid	seeQTL
rs12554847	IPCEF1	trans	lymphoblastoid	seeQTL
rs12554847	DUSP4	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:10107200-10107400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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