Variant report

Variant	rs1678657
Chromosome Location	chr6:38742793-38742794
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	chr6:38742135..38744348-chr6:38746866..38748899,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1018437	0.93[JPT][hapmap]
rs1033525	0.83[ASN][1000 genomes]
rs1033526	0.83[ASN][1000 genomes]
rs1157884	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1614699	1.00[ASW][hapmap];1.00[CEU][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[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1630487	0.92[ASN][1000 genomes]
rs1678638	0.93[JPT][hapmap]
rs1678661	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1678667	0.88[ASN][1000 genomes]
rs1678669	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678675	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678717	0.93[JPT][hapmap]
rs1678718	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1678725	0.81[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1678742	0.93[JPT][hapmap]
rs1738177	0.87[JPT][hapmap]
rs1738184	0.93[JPT][hapmap]
rs1738192	0.89[CEU][hapmap];0.93[JPT][hapmap]
rs1738203	0.93[JPT][hapmap]
rs1738231	0.81[JPT][hapmap]
rs1738232	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738236	0.95[ASN][1000 genomes]
rs1738238	0.90[ASN][1000 genomes]
rs1738239	0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1738240	0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1738241	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1738243	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738247	0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1738263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2206860	0.87[JPT][hapmap]
rs2395709	0.93[JPT][hapmap]
rs2746170	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap]
rs4286777	0.89[JPT][hapmap]
rs4380739	0.87[JPT][hapmap]
rs4386804	0.93[JPT][hapmap]
rs4391252	0.93[JPT][hapmap]
rs4443498	0.93[JPT][hapmap]
rs4571559	0.93[JPT][hapmap]
rs4590258	0.93[JPT][hapmap]
rs4711558	0.93[JPT][hapmap]
rs4714193	0.93[JPT][hapmap]
rs6458080	0.93[JPT][hapmap]
rs6458081	0.93[JPT][hapmap]
rs6931736	0.93[JPT][hapmap]
rs761348	0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs769064	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs862422	0.93[JPT][hapmap]
rs862425	0.93[JPT][hapmap]
rs862427	0.89[CEU][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs9296265	0.93[JPT][hapmap]
rs9357290	0.93[JPT][hapmap]
rs9366982	0.93[JPT][hapmap]
rs9369089	0.93[JPT][hapmap]
rs9380789	0.93[JPT][hapmap]
rs9380791	0.81[JPT][hapmap]
rs9380796	0.93[JPT][hapmap]
rs9380798	0.93[JPT][hapmap]
rs9380799	0.93[JPT][hapmap]
rs9394531	0.87[JPT][hapmap]
rs9394547	0.93[JPT][hapmap]
rs9394550	0.93[JPT][hapmap]
rs982705	0.81[CHD][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1678657	TFEB	cis	parietal	SCAN
rs1678657	CPNE5	cis	cerebellum	SCAN
rs1678657	GUCA1B	cis	cerebellum	SCAN
rs1678657	GNB2	trans	parietal	SCAN
rs1678657	APOBEC2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38739400-38746600	Weak transcription	K562	blood
2	chr6:38739600-38744600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:38739800-38743800	Weak transcription	NHEK	skin
4	chr6:38739800-38744200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38739800-38744200	Weak transcription	HUVEC	blood vessel
6	chr6:38739800-38744400	Weak transcription	HMEC	breast
7	chr6:38740200-38743800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:38741000-38744600	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:38741800-38743800	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:38742400-38743400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:38742600-38742800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:38742600-38743000	Enhancers	Primary B cells from cord blood	blood
13	chr6:38742600-38743200	Enhancers	Monocytes-CD14+_RO01746	blood

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