Variant report

Variant	rs6740110
Chromosome Location	chr2:54959092-54959093
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54956388..54959275-chr2:55046945..55049769,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169439	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175967	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10176359	0.92[CEU][hapmap]
rs10188185	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10194108	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11883962	0.89[EUR][1000 genomes]
rs11888644	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892236	0.80[CEU][hapmap]
rs11904679	0.85[CEU][hapmap]
rs12713273	0.85[CEU][hapmap]
rs12713276	0.90[EUR][1000 genomes]
rs13391803	0.85[CEU][hapmap]
rs13419761	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13428703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046077	0.85[CEU][hapmap]
rs17046108	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs17046149	0.84[EUR][1000 genomes]
rs17046257	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2048370	0.85[CEU][hapmap]
rs2229503	0.85[CEU][hapmap]
rs2271329	0.85[CEU][hapmap]
rs2567834	0.88[ASN][1000 genomes]
rs33946849	0.84[EUR][1000 genomes]
rs34272251	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34456795	0.86[EUR][1000 genomes]
rs354232	0.81[GIH][hapmap]
rs3739109	0.92[CEU][hapmap]
rs58878579	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545430	0.85[CEU][hapmap]
rs6545435	0.85[CEU][hapmap]
rs6545440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732751	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734445	0.85[CEU][hapmap]
rs6734536	0.85[CEU][hapmap]
rs6744586	0.86[EUR][1000 genomes]
rs6752720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67909358	0.89[EUR][1000 genomes]
rs7569127	0.92[CEU][hapmap]
rs7582640	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7584223	0.85[CEU][hapmap]
rs9917248	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6740110	EML6	cis	Thyroid	GTEx
rs6740110	RPL23AP32	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54954600-54965000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:54956800-54964800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:54956800-54964800	Weak transcription	HepG2	liver

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