Variant report

Variant	rs6546790
Chromosome Location	chr2:73084802-73084803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10211019	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1027848	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	0.91[CEU][hapmap]
rs10865393	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150500	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1161265	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1161267	1.00[CEU][hapmap]
rs11684985	0.84[CEU][hapmap]
rs11894160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12474728	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622275	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12713775	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12989141	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12996406	0.91[CEU][hapmap]
rs13035731	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567230	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2048170	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	0.91[CEU][hapmap]
rs2135985	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420880	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420881	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420883	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421095	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4321391	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852298	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap]
rs4852893	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4852902	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546782	0.91[CEU][hapmap]
rs6546783	0.91[CEU][hapmap]
rs6546786	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546788	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546789	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546791	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546792	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730083	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6739002	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6750740	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6758431	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758542	0.86[AMR][1000 genomes];0.98[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];0.82[EUR][1000 genomes]
rs7586787	0.94[EUR][1000 genomes]
rs7588602	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7592155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs925146	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925147	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925148	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
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
rs6546790	MPHOSPH10	cis	cerebellum	SCAN
rs6546790	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:5 , 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	chr2:73084400-73085000	Enhancers	Fetal Heart	heart
5	chr2:73084800-73085000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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