Variant report

Variant	rs7592044
Chromosome Location	chr2:9870631-9870632
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	chr2:9870027..9872978-chr2:9873410..9875751,2	K562	blood:
2	chr2:9845674..9847302-chr2:9868513..9870809,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10164660	0.90[ASN][1000 genomes]
rs10178017	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10200779	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10202938	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929596	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10929597	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10929598	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10929600	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929602	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929605	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929607	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10929608	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10929609	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1123269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs11674024	0.80[ASN][1000 genomes]
rs11674642	0.95[JPT][hapmap]
rs11676286	0.80[ASN][1000 genomes]
rs11680429	0.95[JPT][hapmap]
rs11695437	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892176	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11901380	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11902412	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11902608	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12466594	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12470409	0.80[ASN][1000 genomes]
rs12472594	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475853	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs12476232	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs12991432	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12993968	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13024852	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13028425	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13395171	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13398163	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13398193	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13398304	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1877949	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1877950	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877951	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877953	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357263	0.86[CEU][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2357264	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357265	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4459704	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4507070	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4668636	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4668637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4668638	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668639	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668640	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4668642	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4668643	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669430	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669432	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669433	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669435	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669437	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669441	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669445	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669447	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669448	0.80[ASN][1000 genomes]
rs5020306	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58577971	0.81[ASN][1000 genomes]
rs58961346	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6432033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6712077	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6724483	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727688	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6735280	0.95[JPT][hapmap]
rs6736421	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752842	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6756567	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7423455	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7578933	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7602784	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605675	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs885572	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7592044	PDIA6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9869600-9875800	Weak transcription	Fetal Thymus	thymus
2	chr2:9869800-9871200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:9870400-9870800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:9870400-9870800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:9870600-9870800	Enhancers	K562	blood

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