Variant report

Variant	rs2838997
Chromosome Location	chr21:47216919-47216920
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47208812..47212516-chr21:47213678..47217597,6	K562	blood:
2	chr21:47212372..47214255-chr21:47215488..47217482,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC19A1-11	chr21:47216897-47217493	NONHSAT082994
2	lnc-COL6A1-9	chr21:47216897-47218723	NONHSAT082995

Extended variants
information (count: 109 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11089024	0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs12329855	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12481867	0.93[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs12481913	0.93[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12482094	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs12482377	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482405	0.84[ASN][1000 genomes]
rs12482648	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12482750	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12482853	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1467758	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17351433	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2065334	1.00[JPT][hapmap]
rs2094888	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2183595	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.91[ASN][1000 genomes]
rs2183596	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs2838973	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2838974	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838976	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838982	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838989	0.89[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs2838990	0.91[ASN][1000 genomes]
rs2838991	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2838992	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs2838993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[ASN][1000 genomes]
rs2838994	0.89[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.88[ASN][1000 genomes]
rs2838995	0.93[ASN][1000 genomes]
rs2838996	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838998	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838999	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839000	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839001	0.95[ASN][1000 genomes]
rs2839002	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839003	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839004	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839009	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839013	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2839014	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2839026	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839029	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839032	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28583990	0.86[ASN][1000 genomes]
rs3367	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs35781238	0.93[ASN][1000 genomes]
rs3788211	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788216	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3788220	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788224	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3788227	0.93[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs3920695	0.80[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs4434082	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4818798	0.92[ASN][1000 genomes]
rs4818801	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819151	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819152	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs55707606	0.93[ASN][1000 genomes]
rs55780126	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55875620	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55927540	0.81[ASN][1000 genomes]
rs56012600	0.86[ASN][1000 genomes]
rs56036552	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56256701	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56323347	0.91[ASN][1000 genomes]
rs56347571	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56378934	0.93[ASN][1000 genomes]
rs58952758	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59398815	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59785950	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60604183	0.91[ASN][1000 genomes]
rs61100346	0.93[ASN][1000 genomes]
rs62213555	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62214592	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214596	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214597	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214599	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214604	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66552772	0.93[ASN][1000 genomes]
rs66991496	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7276632	0.91[ASN][1000 genomes]
rs8127369	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8127428	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs8127809	0.92[ASN][1000 genomes]
rs8128722	0.89[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs914241	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs9306139	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs9637205	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637206	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637208	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9647230	0.91[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs9974491	0.91[ASN][1000 genomes]
rs9977309	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9977908	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9978078	0.91[ASN][1000 genomes]
rs9978740	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2838997	TRPM2	cis	cerebellum	SCAN
rs2838997	PCBP3	cis	lung	GTEx
rs2838997	PCBP3	cis	Heart Left Ventricle	GTEx
rs2838997	COL6A1	cis	parietal	SCAN
rs2838997	PCBP3	cis	Muscle Skeletal	GTEx
rs2838997	COL6A1	cis	cerebellum	SCAN
rs2838997	PCBP3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47199400-47217200	Weak transcription	Spleen	Spleen
2	chr21:47208000-47217200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:47209200-47217200	Weak transcription	Gastric	stomach
4	chr21:47209600-47217200	Weak transcription	Pancreas	Pancrea
5	chr21:47213400-47217200	Weak transcription	Thymus	Thymus
6	chr21:47213400-47219800	Weak transcription	Fetal Thymus	thymus
7	chr21:47213800-47217000	Weak transcription	Fetal Kidney	kidney

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