Variant report

Variant	rs6546786
Chromosome Location	chr2:73084019-73084020
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: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10211019	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1027848	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	0.91[CEU][hapmap]
rs10865393	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1150500	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs1161265	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs1161266	0.86[AMR][1000 genomes]
rs1161267	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs11684985	0.84[CEU][hapmap]
rs11894160	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12474728	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622275	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12713775	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12989141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12996406	0.91[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs13035731	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567230	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	0.91[CEU][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2048170	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	0.91[CEU][hapmap]
rs2135985	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420880	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420881	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420883	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2421095	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4321391	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852298	0.91[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs4852893	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4852902	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546782	0.91[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs6546783	0.91[CEU][hapmap]
rs6546788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546789	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546790	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546791	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546792	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730083	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6739002	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6750740	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6758431	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758542	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571064	0.84[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap]
rs7580268	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7586787	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7588602	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7592155	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs925146	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925147	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925148	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970577	1.00[YRI][hapmap]
rs990569	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[TSI][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
rs6546786	MPHOSPH10	cis	cerebellum	SCAN
rs6546786	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73079000-73088200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:73082200-73088200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:73082600-73088000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:73083800-73084200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:73083800-73084400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr2:73084000-73084400	Enhancers	H1 Cell Line	embryonic stem cell

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