Variant report

Variant	rs1570595
Chromosome Location	chr1:58259463-58259464
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12034235	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323828	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs1323836	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1408141	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1408146	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1570596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581763	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1886142	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1886143	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1924268	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6698015	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7533341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs852749	0.95[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852753	0.95[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs852760	0.94[CEU][hapmap]
rs852764	0.90[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852765	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852766	0.95[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852767	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852773	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852776	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852777	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852780	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852781	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs852783	0.95[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852786	0.95[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs927613	0.85[ASN][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	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv829937	chr1:58258288-58406506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1570595	TTC22	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58257600-58262400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:58258000-58262400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:58259000-58259800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:58259400-58259800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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