Variant report

Variant	rs2798053
Chromosome Location	chr9:93142567-93142568
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	chr9:93140741..93143322-chr9:93148992..93151722,2	K562	blood:
2	chr9:93141218..93144173-chr9:93173013..93175871,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10761349	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761373	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10821371	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821391	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821443	0.89[CEU][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs10821444	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs10993252	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993310	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993468	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10993469	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1329090	0.85[ASN][1000 genomes]
rs1343100	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343101	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1571452	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627667	0.90[ASN][1000 genomes]
rs1630044	0.88[ASN][1000 genomes]
rs1648473	0.88[ASN][1000 genomes]
rs1648475	0.90[ASN][1000 genomes]
rs1648476	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1754054	0.90[ASN][1000 genomes]
rs1754055	0.90[ASN][1000 genomes]
rs1754056	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1754059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1776994	0.90[ASN][1000 genomes]
rs1776995	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1777013	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1777035	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1889205	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983962	0.88[ASN][1000 genomes]
rs2004205	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386534	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555061	0.90[ASN][1000 genomes]
rs2555065	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555066	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555067	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555068	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2771077	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2771080	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2771081	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2798043	0.88[ASN][1000 genomes]
rs2798049	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798050	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748185	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3748186	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3748187	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6479595	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs752788	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7862861	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7870764	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs9332454	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]

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	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv528155	chr9:93106543-93152717	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2798053	ECM2	cis	parietal	SCAN
rs2798053	RP11-389K14.3	cis	lung	GTEx
rs2798053	DIRAS2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93141600-93142800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:93142200-93142600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:93142400-93143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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