Variant report

Variant	rs10020998
Chromosome Location	chr4:106428454-106428455
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	chr4:106427208..106429794-chr4:106628992..106631522,2	MCF-7	breast:
2	chr4:106066457..106069377-chr4:106426746..106429457,2	K562	blood:

Variant related genes	Relation type
ENSG00000138780	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10007134	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10024331	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap]
rs1125254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11934602	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2023840	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2046880	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2298732	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2636693	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[TSI][hapmap]
rs2636694	0.87[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap]
rs2713826	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2866883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34248474	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[TSI][hapmap]
rs35775499	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3864225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4235414	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4699176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699178	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533196	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533197	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533198	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533201	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6836448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs763289	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678401	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7691192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8180199	0.92[ASN][1000 genomes]
rs981136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9990819	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999896	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10020998	PPA2	cis	multi-tissue	Pritchard
rs10020998	PPA2	cis	Lymphoblastoid	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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