Variant report

Variant	rs636389
Chromosome Location	chr6:56288616-56288617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56282151..56283969-chr6:56288478..56291005,2	MCF-7	breast:
2	chr6:56263704..56266113-chr6:56287391..56289066,2	MCF-7	breast:
3	chr6:56288567..56292393-chr6:56296577..56299834,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000220666	Chromatin interaction
ENSG00000266793	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11751569	0.90[YRI][hapmap]
rs11757910	0.89[YRI][hapmap]
rs11757941	0.90[YRI][hapmap]
rs11758339	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs11759493	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs13218268	0.90[YRI][hapmap]
rs2143349	0.81[CHB][hapmap]
rs2294697	0.83[MKK][hapmap];0.90[YRI][hapmap]
rs2397221	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2397226	0.83[YRI][hapmap]
rs4130060	0.83[YRI][hapmap]
rs4143828	0.91[YRI][hapmap]
rs4715620	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715623	0.80[ASN][1000 genomes]
rs4715630	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs595238	1.00[YRI][hapmap]
rs601783	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603164	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs604857	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs611044	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs619485	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633348	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459158	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs646336	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs649982	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs659697	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911502	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6915564	0.95[CEU][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs6936834	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7741295	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs7762629	0.91[YRI][hapmap]
rs7775847	0.95[CEU][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9296848	0.87[ASW][hapmap]
rs9370535	0.83[YRI][hapmap]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1022577	chr6:56263674-56289698	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs636389	TRAM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56288200-56289600	Enhancers	Ovary	ovary
2	chr6:56288600-56289600	Enhancers	Stomach Smooth Muscle	stomach
3	chr6:56288600-56290400	Enhancers	Fetal Heart	heart

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