Variant report

Variant	rs6033950
Chromosome Location	chr20:1487850-1487851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1445622..1448578-chr20:1487118..1490074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1543423	0.83[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1883934	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1884387	0.82[ASN][1000 genomes]
rs2143832	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2873565	0.82[ASN][1000 genomes]
rs3795134	0.80[JPT][hapmap]
rs6033860	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs6033867	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6033901	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6033910	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033949	0.81[ASN][1000 genomes]
rs6033951	0.89[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042462	0.81[JPT][hapmap]
rs6042500	0.82[ASN][1000 genomes]
rs6042544	0.83[CHB][hapmap]
rs6042592	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6042602	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6042611	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042650	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042667	0.89[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs6042675	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs6074709	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6074715	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6074718	0.97[ASN][1000 genomes]
rs6079277	0.82[ASN][1000 genomes]
rs6079288	0.82[ASN][1000 genomes]
rs6079289	0.82[ASN][1000 genomes]
rs6079294	0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6079302	0.82[ASN][1000 genomes]
rs6079325	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs6079330	0.88[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079336	0.88[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079354	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6079361	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6079362	0.88[ASN][1000 genomes]
rs6079376	0.89[ASN][1000 genomes]
rs6105233	0.87[ASN][1000 genomes]
rs6105234	0.88[ASN][1000 genomes]
rs6105240	0.97[ASN][1000 genomes]
rs6110169	0.85[ASN][1000 genomes]
rs6110207	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6110215	0.88[ASN][1000 genomes]
rs6110226	0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6110228	0.92[ASN][1000 genomes]
rs6110253	0.97[ASN][1000 genomes]
rs6110261	0.98[ASN][1000 genomes]
rs6110262	0.97[ASN][1000 genomes]
rs6131543	0.82[ASN][1000 genomes]
rs6131553	0.84[ASN][1000 genomes]
rs6131559	0.87[ASN][1000 genomes]
rs6135033	0.80[JPT][hapmap]
rs6135048	0.82[ASN][1000 genomes]
rs6135050	0.82[ASN][1000 genomes]
rs6135060	0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6135061	0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6135062	0.83[ASN][1000 genomes]
rs6135063	0.82[ASN][1000 genomes]
rs6135064	0.84[ASN][1000 genomes]
rs6135068	0.85[ASN][1000 genomes]
rs6135069	0.85[ASN][1000 genomes]
rs6135080	0.85[ASN][1000 genomes]
rs6135089	0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6135095	0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6135105	0.88[ASN][1000 genomes]
rs7270432	0.97[ASN][1000 genomes]
rs963867	0.89[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6033950	SPEF1	cis	parietal	SCAN
rs6033950	RP4-776F14.3	cis	Whole Blood	GTEx
rs6033950	SIRPB2	cis	Whole Blood	GTEx
rs6033950	NSFL1C	cis	cerebellum	SCAN
rs6033950	NSFL1C	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1482000-1497600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:1484200-1488600	Enhancers	HMEC	breast
3	chr20:1484200-1489200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:1485600-1489400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:1486800-1489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:1486800-1489600	Enhancers	NHEK	skin
7	chr20:1487200-1489200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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