Variant report

Variant	rs1857401
Chromosome Location	chr1:216762158-216762159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216755828..216757414-chr1:216760890..216762450,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10218694	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863256	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10863258	0.87[ASN][1000 genomes]
rs11117627	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11117628	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12087642	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12088947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1414530	0.83[MEX][hapmap]
rs1419242	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1498276	0.83[MEX][hapmap]
rs1833038	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1833040	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2377106	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4846546	0.92[ASN][1000 genomes]
rs6673566	0.83[MEX][hapmap]
rs6701062	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519402	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7533692	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7544758	0.88[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7546236	0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap]
rs7553212	0.86[JPT][hapmap]
rs951034	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873178	chr1:216714314-216813244	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv4565	chr1:216720070-216765053	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv468138	chr1:216736138-216762158	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv549203	chr1:216736138-216762158	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1857401	DTL	cis	cerebellum	SCAN
rs1857401	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216721800-216774000	Weak transcription	Placenta	Placenta
2	chr1:216744800-216764600	Weak transcription	Left Ventricle	heart
3	chr1:216755200-216767800	Weak transcription	Fetal Heart	heart
4	chr1:216757400-216773600	Weak transcription	Fetal Intestine Small	intestine

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