Variant report

Variant	rs6582337
Chromosome Location	chr12:41899312-41899313
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:41899238-41899378	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PDZRN4	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10161143	0.93[AMR][1000 genomes]
rs10506194	1.00[EUR][1000 genomes]
rs10506196	1.00[EUR][1000 genomes]
rs10880084	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs10880090	1.00[EUR][1000 genomes]
rs11180887	0.81[JPT][hapmap]
rs11180888	0.90[JPT][hapmap]
rs11180903	1.00[GIH][hapmap]
rs11180917	1.00[GIH][hapmap]
rs11180947	1.00[GIH][hapmap]
rs11180948	1.00[GIH][hapmap]
rs11180969	1.00[GIH][hapmap]
rs11180970	1.00[EUR][1000 genomes]
rs11180971	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11180972	1.00[EUR][1000 genomes]
rs11180973	1.00[EUR][1000 genomes]
rs11180974	1.00[EUR][1000 genomes]
rs11180975	1.00[EUR][1000 genomes]
rs11180976	1.00[EUR][1000 genomes]
rs11180978	1.00[EUR][1000 genomes]
rs11180982	1.00[EUR][1000 genomes]
rs11180983	1.00[EUR][1000 genomes]
rs11180995	1.00[EUR][1000 genomes]
rs11180997	1.00[EUR][1000 genomes]
rs11181000	1.00[EUR][1000 genomes]
rs12227540	1.00[EUR][1000 genomes]
rs12298553	0.88[AMR][1000 genomes]
rs12300549	0.86[AMR][1000 genomes]
rs12305318	0.86[AMR][1000 genomes]
rs12307517	0.88[AMR][1000 genomes]
rs12314242	0.84[AMR][1000 genomes]
rs12314805	0.84[AMR][1000 genomes]
rs12581707	1.00[EUR][1000 genomes]
rs1350433	0.91[MEX][hapmap];0.93[AMR][1000 genomes]
rs1379766	1.00[GIH][hapmap]
rs1458155	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs1458172	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1458173	1.00[EUR][1000 genomes]
rs17129267	0.90[MEX][hapmap]
rs17129347	0.91[MEX][hapmap]
rs17129351	0.90[AMR][1000 genomes]
rs17129364	0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs17129405	0.91[MEX][hapmap];0.95[AMR][1000 genomes]
rs17129413	0.93[AMR][1000 genomes]
rs17129436	1.00[EUR][1000 genomes]
rs17129441	0.90[AMR][1000 genomes]
rs17835484	1.00[EUR][1000 genomes]
rs1817270	0.91[MEX][hapmap];0.88[AMR][1000 genomes]
rs2034922	0.90[AMR][1000 genomes]
rs2125289	1.00[EUR][1000 genomes]
rs2252312	1.00[EUR][1000 genomes]
rs2405924	0.88[AMR][1000 genomes]
rs2897270	0.93[AMR][1000 genomes]
rs35577124	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3761676	0.90[AMR][1000 genomes]
rs4635145	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57991277	0.90[AMR][1000 genomes]
rs58573939	0.88[AMR][1000 genomes]
rs59662716	0.88[AMR][1000 genomes]
rs59955144	1.00[EUR][1000 genomes]
rs60903037	0.90[AMR][1000 genomes]
rs713288	0.94[CHB][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7297699	0.86[AMR][1000 genomes]
rs7307387	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs731979	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73274484	0.82[AMR][1000 genomes]
rs73278055	0.88[AMR][1000 genomes]
rs74077585	0.88[AMR][1000 genomes]
rs74077591	0.88[AMR][1000 genomes]
rs7960293	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	esv3486330	chr12:41899304-41899798	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41869600-41905200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41877400-41903600	Weak transcription	Ovary	ovary
3	chr12:41887600-41901400	Weak transcription	Brain Substantia Nigra	brain
4	chr12:41894000-41900600	Weak transcription	Brain Germinal Matrix	brain
5	chr12:41898000-41900200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:41898600-41901000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
8	chr12:41899000-41906000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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