Variant report

Variant	rs13000120
Chromosome Location	chr2:55015024-55015025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55013900..55016291-chr2:55017771..55020544,3	MCF-7	breast:
2	chr2:55008139..55011075-chr2:55013927..55016853,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13005723	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006104	0.86[EUR][1000 genomes]
rs13011362	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13033894	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17046343	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17046380	0.90[EUR][1000 genomes]
rs17417134	0.88[EUR][1000 genomes]
rs17417259	0.88[EUR][1000 genomes]
rs1816376	0.88[EUR][1000 genomes]
rs2116439	0.95[ASN][1000 genomes]
rs34049612	0.81[EUR][1000 genomes]
rs34170608	0.87[EUR][1000 genomes]
rs34389776	0.88[EUR][1000 genomes]
rs35457818	0.88[EUR][1000 genomes]
rs56113416	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66921272	0.90[EUR][1000 genomes]
rs6705883	0.88[EUR][1000 genomes]
rs67248043	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67607054	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72806702	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808606	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv1844727	chr2:54999712-55084583	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv870295	chr2:55008613-55065985	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457908	chr2:55010115-55031023	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv582026	chr2:55010115-55031023	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv470465	chr2:55010115-55034113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv457919	chr2:55010193-55028892	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv582027	chr2:55010193-55028892	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13000120	EML6	cis	Thyroid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55012000-55015200	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:55013600-55015400	Enhancers	Pancreas	Pancrea
3	chr2:55015000-55015400	Enhancers	Gastric	stomach

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