Variant report

Variant	rs1209929
Chromosome Location	chr21:40158941-40158942
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:40158395..40160245-chr21:40285498..40288135,2	MCF-7	breast:
2	chr21:40158041..40161910-chr21:40175596..40180594,8	K562	blood:
3	chr21:39714897..39716784-chr21:40158367..40161064,2	MCF-7	breast:
4	chr21:40158174..40165115-chr21:40166769..40170231,7	K562	blood:
5	chr21:40157809..40160879-chr21:40282729..40285436,3	MCF-7	breast:
6	chr21:40156704..40162526-chr21:40173499..40179988,10	MCF-7	breast:
7	chr21:40158554..40160478-chr21:40163082..40164922,2	K562	blood:
8	chr21:40140717..40143513-chr21:40158331..40160522,2	MCF-7	breast:
9	chr21:40156369..40159602-chr21:40175863..40178894,4	K562	blood:
10	chr21:40145518..40147915-chr21:40158381..40160685,2	K562	blood:
11	chr21:40158554..40160744-chr21:40179736..40182469,2	MCF-7	breast:
12	chr21:40156601..40161503-chr21:40174870..40178905,10	MCF-7	breast:
13	chr21:40021665..40023567-chr21:40158455..40160815,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction
ENSG00000234035	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1013777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1041438	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1041781	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1041782	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11088448	0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1209912	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1209913	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1209914	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1209916	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209917	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]
rs1209918	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1209919	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1209920	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1209921	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1209922	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209923	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209924	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209925	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]
rs1209926	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]
rs1209927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209931	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209935	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209936	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209937	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209942	0.91[ASN][1000 genomes]
rs1209943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209944	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209945	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209946	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209947	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12626796	0.81[ASN][1000 genomes]
rs13047789	0.82[ASN][1000 genomes]
rs1309152	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]
rs16996828	0.81[YRI][hapmap]
rs2000638	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];0.95[JPT][hapmap]
rs2283639	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7278110	0.81[YRI][hapmap]

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	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	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
3	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
4	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
5	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
6	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
7	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
rs1209929	ETS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40153000-40159200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:40156200-40159200	Enhancers	HepG2	liver
3	chr21:40156200-40159800	Enhancers	Stomach Mucosa	stomach
4	chr21:40156200-40163600	Enhancers	Fetal Intestine Small	intestine
5	chr21:40156400-40163200	Enhancers	Fetal Intestine Large	intestine
6	chr21:40157400-40159200	Weak transcription	Liver	Liver
7	chr21:40157600-40159200	Weak transcription	Pancreas	Pancrea
8	chr21:40157800-40159600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr21:40157800-40159600	Enhancers	GM12878-XiMat	blood
10	chr21:40157800-40160200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr21:40157800-40161800	Weak transcription	Fetal Lung	lung
12	chr21:40158000-40159600	Enhancers	A549	lung
13	chr21:40158200-40159400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr21:40158200-40159600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr21:40158200-40160200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr21:40158200-40161200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr21:40158400-40159600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr21:40158400-40160200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr21:40158400-40160200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr21:40158400-40160400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr21:40158600-40159200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:40158600-40159200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr21:40158600-40159600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr21:40158600-40159800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr21:40158600-40159800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr21:40158600-40161000	Weak transcription	Small Intestine	intestine
27	chr21:40158800-40159000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr21:40158800-40159600	Enhancers	Hela-S3	cervix
29	chr21:40158800-40159600	Enhancers	NHEK	skin

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