Variant report

Variant	rs1209917
Chromosome Location	chr21:40153750-40153751
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40151697..40154341-chr21:40177180..40179179,3	K562	blood:
2	chr21:40106344..40108151-chr21:40152083..40153978,2	MCF-7	breast:
3	chr21:40151697..40154341-chr21:40177555..40180679,4	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1013777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1041438	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1041781	0.90[ASN][1000 genomes]
rs1041782	0.90[ASN][1000 genomes]
rs11088448	0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1209912	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1209913	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1209914	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1209916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209918	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209921	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209922	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209923	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209924	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209931	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1209935	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209936	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1209937	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209938	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209939	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209940	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209942	0.90[ASN][1000 genomes]
rs1209943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209944	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1209945	0.90[ASN][1000 genomes]
rs1209946	0.90[ASN][1000 genomes]
rs1209947	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13047789	0.81[ASN][1000 genomes]
rs1309152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2000638	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156422	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs2256290	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs2283638	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2283639	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9981039	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060405	chr21:40095523-40159813	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv913740	chr21:40103951-40157124	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1060535	chr21:40114130-40155067	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1063936	chr21:40114130-40159150	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv459258	chr21:40116044-40157124	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv587476	chr21:40116044-40157124	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv913742	chr21:40116044-40157124	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv516348	chr21:40116044-40161381	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv913743	chr21:40116044-40161381	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1055623	chr21:40118451-40161072	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1056485	chr21:40128875-40159813	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1209917	ETS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40147600-40158200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr21:40152000-40153800	Enhancers	Hela-S3	cervix
3	chr21:40152400-40154000	Enhancers	HepG2	liver
4	chr21:40152600-40153800	Enhancers	Fetal Intestine Small	intestine
5	chr21:40152600-40153800	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr21:40152600-40154000	Enhancers	Fetal Intestine Large	intestine
7	chr21:40153000-40159200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:40153400-40154000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:40153400-40154000	ZNF genes & repeats	GM12878-XiMat	blood
10	chr21:40153600-40154000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr21:40153600-40154000	Enhancers	Duodenum Mucosa	Duodenum

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