Variant report

Variant	rs1527400
Chromosome Location	chr2:178522011-178522012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178521915..178523985-chr2:178527127..178529647,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10497493	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11680632	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618150	0.96[YRI][hapmap]
rs12618542	0.82[CHB][hapmap]
rs12619453	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13000926	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13017429	0.96[YRI][hapmap]
rs13019660	1.00[CHB][hapmap]
rs13025391	1.00[ASW][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs13025904	1.00[ASW][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs13026012	0.84[AFR][1000 genomes]
rs13028757	1.00[ASW][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs1358326	0.93[ASW][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs1358327	0.96[YRI][hapmap]
rs1405716	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527398	0.85[CHD][hapmap]
rs1527399	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527402	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534304	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap]
rs1544001	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs1544003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547582	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865535	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1997206	0.96[YRI][hapmap]
rs1997208	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1997209	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap]
rs2365619	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2365620	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2886422	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770003	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4110134	0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs4341975	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs4893974	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4893975	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4893977	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433683	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433685	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs6433687	0.93[ASW][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap]
rs6433688	0.84[GIH][hapmap]
rs6721360	0.96[YRI][hapmap]
rs6730406	0.91[CHD][hapmap];0.85[MEX][hapmap]
rs6734426	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs6755382	0.81[AFR][1000 genomes]
rs7422544	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560080	0.96[YRI][hapmap]
rs7560514	0.96[YRI][hapmap]
rs7560737	0.93[ASW][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs7577174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578901	0.96[YRI][hapmap]
rs7586934	0.93[ASW][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs7591796	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591897	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594290	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7597640	0.96[YRI][hapmap]
rs941271	0.96[YRI][hapmap]
rs941276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1527400	AGPS	cis	cerebellum	SCAN
rs1527400	TTC30B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178517000-178524400	Weak transcription	Fetal Kidney	kidney
2	chr2:178517200-178530800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:178517400-178524200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:178518600-178524400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:178519000-178524400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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