Variant report

Variant	rs1209925
Chromosome Location	chr21:40156990-40156991
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40156267..40158669-chr21:40161958..40164607,2	K562	blood:
2	chr21:40156704..40162526-chr21:40173499..40179988,10	MCF-7	breast:
3	chr21:40156379..40158519-chr21:40187612..40190020,2	MCF-7	breast:
4	chr21:40156369..40159602-chr21:40175863..40178894,4	K562	blood:
5	chr21:40156601..40161503-chr21:40174870..40178905,10	MCF-7	breast:
6	chr21:40147391..40149413-chr21:40156401..40158337,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1013777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1041438	0.90[EUR][1000 genomes]
rs1041781	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1041782	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11088448	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1209912	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1209913	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1209914	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1209916	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209917	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]
rs1209918	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209919	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209920	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209921	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209922	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209923	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209924	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209926	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209931	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1209935	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209936	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1209937	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209938	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209939	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209940	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209942	0.90[ASN][1000 genomes]
rs1209943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209944	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209945	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209946	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209947	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13047789	0.81[ASN][1000 genomes]
rs1309152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2000638	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156422	0.82[CHB][hapmap]
rs2256290	0.82[CHB][hapmap]
rs2283638	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2283639	0.86[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
rs1209925	ETS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40147600-40158200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr21:40153000-40159200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr21:40153800-40158800	Weak transcription	Hela-S3	cervix
4	chr21:40154600-40158400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr21:40156200-40159200	Enhancers	HepG2	liver
6	chr21:40156200-40159800	Enhancers	Stomach Mucosa	stomach
7	chr21:40156200-40163600	Enhancers	Fetal Intestine Small	intestine
8	chr21:40156400-40158600	Enhancers	Duodenum Mucosa	Duodenum
9	chr21:40156400-40163200	Enhancers	Fetal Intestine Large	intestine
10	chr21:40156800-40157000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr21:40156800-40157000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr21:40156800-40157000	Enhancers	Placenta	Placenta
13	chr21:40156800-40157600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links