Variant report

Variant	rs16990428
Chromosome Location	chr22:32813776-32813777
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	chr22:32807783..32810463-chr22:32811648..32815260,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100220	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs11089557	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11089560	0.82[AMR][1000 genomes]
rs11089564	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11635	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11912349	0.95[ASN][1000 genomes]
rs12160141	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12160986	0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12628702	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs136471	0.97[AMR][1000 genomes]
rs1543320	0.91[CHB][hapmap];0.93[CHD][hapmap]
rs16987625	0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16990258	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16990262	0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16990269	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16990430	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810450	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2014356	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049946	0.83[CHB][hapmap]
rs2072815	0.86[CHB][hapmap]
rs2072816	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2076041	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2076045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281034	0.86[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2281035	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294311	0.92[ASN][1000 genomes]
rs2294313	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs2294314	0.92[ASN][1000 genomes]
rs2413110	0.91[AMR][1000 genomes]
rs2413111	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2413113	0.86[CHB][hapmap]
rs28404482	0.91[AMR][1000 genomes]
rs2899184	0.97[AMR][1000 genomes]
rs2899185	0.86[JPT][hapmap]
rs35207231	0.85[AMR][1000 genomes]
rs4140572	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs45593940	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4577392	0.91[AMR][1000 genomes]
rs5749408	0.82[EUR][1000 genomes]
rs5749409	0.89[GIH][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749410	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749411	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749412	0.81[JPT][hapmap]
rs5749413	0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5749414	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749416	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs5749426	0.82[CHB][hapmap]
rs5749427	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749428	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs5749429	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749433	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749436	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs5753988	0.88[AMR][1000 genomes]
rs5754000	0.94[AMR][1000 genomes]
rs5754001	0.97[AMR][1000 genomes]
rs5754003	0.81[JPT][hapmap];0.97[AMR][1000 genomes]
rs5754005	0.97[AMR][1000 genomes]
rs5754006	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754007	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754008	0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754009	0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes]
rs5754010	0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754011	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754012	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754017	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754018	0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754019	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754021	0.94[AMR][1000 genomes]
rs5754023	0.94[AMR][1000 genomes]
rs5754025	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754027	0.81[JPT][hapmap]
rs5754029	0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754030	0.81[JPT][hapmap]
rs5754031	0.82[AMR][1000 genomes]
rs5754032	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754033	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5754035	0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes]
rs5754036	0.81[JPT][hapmap]
rs5754037	0.81[JPT][hapmap]
rs5754039	0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5754040	0.81[JPT][hapmap]
rs5754042	0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5754044	0.81[JPT][hapmap]
rs5754045	0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5754046	0.82[AMR][1000 genomes]
rs5754047	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5754048	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5754050	0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5754063	0.82[CHB][hapmap]
rs5754065	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5754066	0.82[CHB][hapmap]
rs57606003	0.82[AMR][1000 genomes]
rs58028985	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58500302	0.94[AMR][1000 genomes]
rs58637580	0.82[AMR][1000 genomes]
rs59895149	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5994562	0.83[CHB][hapmap]
rs5998434	0.91[AMR][1000 genomes]
rs5998451	0.81[JPT][hapmap]
rs5998453	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998456	0.80[JPT][hapmap]
rs5998457	0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998459	0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998463	0.81[JPT][hapmap]
rs5998471	0.86[CHB][hapmap]
rs5998475	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs5998478	0.83[CHB][hapmap]
rs713790	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72617300	0.89[AMR][1000 genomes]
rs72617301	0.91[AMR][1000 genomes]
rs72617302	0.97[AMR][1000 genomes]
rs72620403	0.91[AMR][1000 genomes]
rs72620404	0.97[AMR][1000 genomes]
rs72620405	0.97[AMR][1000 genomes]
rs72620406	0.97[AMR][1000 genomes]
rs72620407	0.97[AMR][1000 genomes]
rs72620408	0.97[AMR][1000 genomes]
rs7287452	0.82[CHB][hapmap]
rs7292163	0.82[AMR][1000 genomes]
rs737779	0.86[CHB][hapmap]
rs738267	0.81[JPT][hapmap]
rs742096	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1055701	chr22:32806595-32845403	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16990428	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL
rs16990428	RFPL3S	cis	lymphoblastoid	seeQTL
rs16990428	SLC5A4	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32808200-32818000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr22:32808400-32818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32809000-32814000	Weak transcription	GM12878-XiMat	blood
4	chr22:32809000-32817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:32810200-32817000	Weak transcription	Liver	Liver

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