Variant report

Variant	rs1678718
Chromosome Location	chr6:38793510-38793511
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38791887..38794503-chr6:38904542..38906187,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1018437	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1157884	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1614699	0.93[JPT][hapmap]
rs1630487	0.83[ASN][1000 genomes]
rs1678638	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1678640	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678657	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1678669	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678675	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678717	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1678725	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678727	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678742	0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1738177	0.80[JPT][hapmap]
rs1738184	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1738192	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1738199	0.89[ASN][1000 genomes]
rs1738203	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1738220	0.82[JPT][hapmap]
rs1738231	0.87[JPT][hapmap]
rs1738232	0.85[ASN][1000 genomes]
rs1738236	0.85[ASN][1000 genomes]
rs1738238	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1738239	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1738240	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1738241	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1738243	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738247	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1738263	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2206860	0.84[MKK][hapmap]
rs2395709	1.00[JPT][hapmap]
rs2746170	0.80[JPT][hapmap]
rs4286777	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4380739	0.93[JPT][hapmap]
rs4386804	1.00[JPT][hapmap]
rs4391252	1.00[JPT][hapmap]
rs4443498	1.00[JPT][hapmap]
rs4571559	1.00[JPT][hapmap]
rs4590258	1.00[JPT][hapmap]
rs4711558	1.00[JPT][hapmap]
rs4714193	1.00[JPT][hapmap]
rs6458080	1.00[JPT][hapmap]
rs6458081	1.00[JPT][hapmap]
rs6931736	1.00[JPT][hapmap]
rs761348	0.85[ASN][1000 genomes]
rs769064	0.80[JPT][hapmap]
rs7757460	0.81[ASN][1000 genomes]
rs862422	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs862425	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs862427	1.00[JPT][hapmap]
rs9296265	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9349100	0.82[ASN][1000 genomes]
rs9357290	1.00[JPT][hapmap]
rs9366982	1.00[JPT][hapmap]
rs9369087	0.84[ASN][1000 genomes]
rs9369089	1.00[JPT][hapmap]
rs9380787	0.83[ASN][1000 genomes]
rs9380789	1.00[JPT][hapmap]
rs9380791	0.87[JPT][hapmap]
rs9380795	0.81[ASN][1000 genomes]
rs9380796	1.00[JPT][hapmap]
rs9380798	1.00[JPT][hapmap]
rs9380799	1.00[JPT][hapmap]
rs9394531	0.80[JPT][hapmap]
rs9394544	0.83[ASN][1000 genomes]
rs9394547	1.00[JPT][hapmap]
rs9394550	1.00[JPT][hapmap]
rs982705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs984523	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1678718	MDFI	cis	parietal	SCAN
rs1678718	LRFN2	cis	cerebellum	SCAN
rs1678718	ANKS1A	cis	parietal	SCAN
rs1678718	RPL7L1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38766800-38824400	Weak transcription	K562	blood
2	chr6:38793400-38793800	Enhancers	HepG2	liver
3	chr6:38793400-38797400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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