Variant report

Variant	rs7091429
Chromosome Location	chr10:50173551-50173552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:50173405-50173605	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
WDFY4	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1015717	0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10735228	0.92[CEU][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs10745290	0.85[CEU][hapmap]
rs10776658	0.85[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10776659	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10776660	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857430	0.85[CEU][hapmap]
rs10857661	0.85[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10857662	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs11101572	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11101573	0.92[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs12413832	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877799	0.85[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1877800	0.92[CEU][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs1913516	0.88[CEU][hapmap]
rs2137909	0.85[CEU][hapmap]
rs2137913	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2249429	0.81[CEU][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2249657	0.82[EUR][1000 genomes]
rs2249659	0.82[EUR][1000 genomes]
rs2252811	0.81[CEU][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2255553	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271565	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2292584	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2292585	0.85[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs2457466	0.92[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2458671	0.82[EUR][1000 genomes]
rs2663028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2663067	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2663068	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2671715	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2889709	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750867	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829206	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4317902	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4614357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4838433	0.83[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs61848117	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6537586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537587	0.85[CEU][hapmap]
rs7072344	0.96[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7082322	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7083751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086917	0.85[CEU][hapmap]
rs7093656	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs7098224	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7091429	CSTF2T	cis	parietal	SCAN
rs7091429	WDFY4	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50144600-50196200	Strong transcription	Primary B cells from cord blood	blood
2	chr10:50145000-50193200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr10:50145400-50193200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:50145800-50193400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:50148000-50193600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:50153400-50187800	Strong transcription	GM12878-XiMat	blood
7	chr10:50153600-50193600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:50161600-50177800	Weak transcription	Lung	lung
9	chr10:50163400-50189000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:50172200-50175200	Strong transcription	Primary hematopoietic stem cells	blood
11	chr10:50172400-50174600	Weak transcription	Spleen	Spleen
12	chr10:50172800-50174000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:50173000-50174200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr10:50173200-50178600	Weak transcription	Primary T cells from cord blood	blood

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