Variant report

Variant	rs1021993
Chromosome Location	chr1:209512373-209512374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209505056..209506644-chr1:209510919..209512526,2	K562	blood:
2	chr1:209509164..209510795-chr1:209511355..209513007,2	K562	blood:
3	chr1:209512114..209513913-chr1:209517327..209518870,2	K562	blood:
4	chr1:209382422..209384753-chr1:209511940..209513719,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1027821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1027823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494924	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs1354854	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1395749	0.84[AFR][1000 genomes]
rs1395750	0.94[AFR][1000 genomes]
rs1395751	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395756	0.84[AMR][1000 genomes]
rs1507341	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1542981	0.92[AFR][1000 genomes]
rs1553622	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1553623	0.82[AFR][1000 genomes]
rs1857966	0.85[CHB][hapmap]
rs2245283	0.84[AFR][1000 genomes]
rs2245287	0.83[AFR][1000 genomes]
rs2356722	0.85[CHB][hapmap]
rs2489649	0.84[AFR][1000 genomes]
rs2660636	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2660640	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2660642	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2660643	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2843167	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2843168	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6661759	0.83[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6674103	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674309	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6685289	0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685498	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs906347	0.83[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs906348	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs906349	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs906350	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs906351	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs925077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937874	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs950890	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1021993	PLEKHA6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209506200-209513600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:209506200-209515600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:209506200-209524600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:209508800-209513000	Weak transcription	Fetal Brain Male	brain

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