Variant report

Variant	rs17131285
Chromosome Location	chr1:70873005-70873006
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	chr1:70871257..70873394-chr1:70875235..70877484,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116761	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10465863	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs11209599	0.83[CEU][hapmap]
rs11209600	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs11209602	0.89[AMR][1000 genomes]
rs11209603	0.81[AMR][1000 genomes]
rs11209608	0.84[AMR][1000 genomes]
rs11209611	0.89[AMR][1000 genomes]
rs12028257	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs12030275	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031053	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs12034101	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12036256	0.83[CEU][hapmap]
rs12037272	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs12042565	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12565458	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12565460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1327873	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1969953	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs4560989	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs4650038	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs4650041	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs4650047	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56211824	0.87[AMR][1000 genomes]
rs58997663	0.84[AMR][1000 genomes]
rs59821213	0.87[AMR][1000 genomes]
rs61122312	0.86[AMR][1000 genomes]
rs61587863	0.84[AMR][1000 genomes]
rs61678482	0.87[AMR][1000 genomes]
rs6686181	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs72678630	0.87[AMR][1000 genomes]
rs72678644	0.87[AMR][1000 genomes]
rs72678645	0.87[AMR][1000 genomes]
rs72678646	0.89[AMR][1000 genomes]
rs72680732	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539544	0.83[CEU][hapmap];0.91[AMR][1000 genomes]
rs768433	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs998523	0.83[CEU][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	esv1797324	chr1:70858435-70876569	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
4	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17131285	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs17131285	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70871600-70875800	Weak transcription	HUVEC	blood vessel
2	chr1:70871800-70875800	Weak transcription	Fetal Lung	lung
3	chr1:70872800-70875200	Weak transcription	Liver	Liver
4	chr1:70872800-70875800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:70872800-70876000	Weak transcription	Adipose Nuclei	Adipose

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