Variant report

Variant	rs1209940
Chromosome Location	chr21:40167062-40167063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40159408..40162072-chr21:40163674..40168810,7	MCF-7	breast:
2	chr21:40158174..40165115-chr21:40166769..40170231,7	K562	blood:
3	chr21:40165875..40171413-chr21:40174363..40179390,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1013777	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1041781	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1041782	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11088448	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1209912	0.81[ASN][1000 genomes]
rs1209913	0.82[ASN][1000 genomes]
rs1209914	0.83[CHB][hapmap]
rs1209916	0.91[ASN][1000 genomes]
rs1209917	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209918	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209919	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209920	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209921	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209922	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209923	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209924	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209925	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209926	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209927	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209928	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209929	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209931	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209932	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209933	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209934	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209935	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209936	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1209937	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209938	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209939	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209942	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209943	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209945	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209946	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209947	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12626796	0.87[ASN][1000 genomes]
rs13047789	0.88[ASN][1000 genomes]
rs1309152	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2156422	0.87[CHB][hapmap]
rs2256290	0.87[CHB][hapmap]
rs2283638	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2283639	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs714781	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1209940	ETS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40160200-40167400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr21:40160600-40169200	Weak transcription	Placenta	Placenta
3	chr21:40162400-40167400	Weak transcription	K562	blood
4	chr21:40162800-40167200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr21:40163000-40170400	Weak transcription	Colonic Mucosa	Colon
6	chr21:40163000-40171400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr21:40163400-40167200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr21:40163400-40175400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr21:40163600-40167400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40164400-40171200	Enhancers	Duodenum Mucosa	Duodenum
11	chr21:40164600-40167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr21:40164600-40167800	Enhancers	Stomach Mucosa	stomach
13	chr21:40165000-40176600	Enhancers	Fetal Intestine Large	intestine
14	chr21:40165600-40171000	Enhancers	HepG2	liver
15	chr21:40165800-40167800	Enhancers	Esophagus	oesophagus
16	chr21:40165800-40168400	Enhancers	A549	lung
17	chr21:40165800-40169200	Enhancers	Hela-S3	cervix
18	chr21:40166000-40167600	Enhancers	Liver	Liver
19	chr21:40166200-40170800	Weak transcription	Small Intestine	intestine
20	chr21:40166400-40175400	Enhancers	Fetal Intestine Small	intestine
21	chr21:40166400-40176000	Weak transcription	Pancreas	Pancrea
22	chr21:40166600-40177000	Weak transcription	Gastric	stomach
23	chr21:40166800-40171600	Enhancers	NHEK	skin
24	chr21:40167000-40171200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr21:40167000-40174600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:40167000-40176600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links