Variant report

Variant	rs1508060
Chromosome Location	chr2:73078673-73078674
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	chr2:73077050..73079715-chr2:73082762..73084419,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11126381	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11126384	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11686536	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11693376	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11886503	0.92[ASN][1000 genomes]
rs12476137	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12479094	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12614041	0.92[ASN][1000 genomes]
rs12615163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12615875	0.92[ASN][1000 genomes]
rs12994646	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13008515	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1396107	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1532970	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1876489	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1876490	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2068410	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2135982	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2420882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35666345	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4597553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4852891	0.80[CEU][hapmap]
rs4852896	0.89[ASN][1000 genomes]
rs4852900	0.84[ASN][1000 genomes]
rs56181835	0.92[ASN][1000 genomes]
rs56711961	0.92[ASN][1000 genomes]
rs6546787	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6727086	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6744758	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6758539	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6758802	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7577528	0.81[ASN][1000 genomes]
rs7583914	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7586886	0.89[ASN][1000 genomes]
rs7600718	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs970577	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1508060	TGFA	cis	cerebellum	SCAN
rs1508060	STAMBP	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73073800-73079200	Enhancers	Placenta	Placenta
2	chr2:73078200-73078800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:73078200-73079200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:73078200-73079200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:73078400-73078800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:73078600-73078800	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr2:73078600-73079000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:73078600-73079000	Enhancers	HUES6 Cell Line	embryonic stem cell

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