Variant report

Variant	rs1209944
Chromosome Location	chr21:40169706-40169707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40168506..40170347-chr21:40280302..40282000,2	MCF-7	breast:
2	chr21:40158174..40165115-chr21:40166769..40170231,7	K562	blood:
3	chr21:40165875..40171413-chr21:40174363..40179390,12	MCF-7	breast:
4	chr21:40168886..40171203-chr21:40171333..40173388,2	MCF-7	breast:
5	chr21:40164946..40166876-chr21:40169139..40171967,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1013777	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1041781	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1041782	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11088448	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1209912	0.81[ASN][1000 genomes]
rs1209913	0.81[ASN][1000 genomes]
rs1209914	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs1209916	0.90[ASN][1000 genomes]
rs1209917	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1209918	0.89[ASN][1000 genomes]
rs1209919	0.89[ASN][1000 genomes]
rs1209920	0.89[ASN][1000 genomes]
rs1209921	0.89[ASN][1000 genomes]
rs1209922	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209923	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209924	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209925	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209926	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209927	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1209928	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209929	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209931	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209932	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209933	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209934	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209935	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209936	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1209937	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1209938	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209939	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209940	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]
rs1209942	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209945	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209946	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209947	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209949	0.80[ASN][1000 genomes]
rs1209951	0.80[ASN][1000 genomes]
rs1209952	0.82[CHD][hapmap]
rs1209954	0.83[CHD][hapmap]
rs12626796	0.87[ASN][1000 genomes]
rs13047789	0.89[ASN][1000 genomes]
rs1309152	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2156422	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs2256290	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs2283638	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2283639	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs714781	0.86[ASN][1000 genomes]
rs9981039	0.84[CHD][hapmap]

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
rs1209944	ETS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40163000-40170400	Weak transcription	Colonic Mucosa	Colon
2	chr21:40163000-40171400	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr21:40163400-40175400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr21:40164400-40171200	Enhancers	Duodenum Mucosa	Duodenum
5	chr21:40165000-40176600	Enhancers	Fetal Intestine Large	intestine
6	chr21:40165600-40171000	Enhancers	HepG2	liver
7	chr21:40166200-40170800	Weak transcription	Small Intestine	intestine
8	chr21:40166400-40175400	Enhancers	Fetal Intestine Small	intestine
9	chr21:40166400-40176000	Weak transcription	Pancreas	Pancrea
10	chr21:40166600-40177000	Weak transcription	Gastric	stomach
11	chr21:40166800-40171600	Enhancers	NHEK	skin
12	chr21:40167000-40171200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:40167000-40174600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr21:40167000-40176600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:40167200-40171600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr21:40167600-40171000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr21:40167600-40175400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:40168000-40169800	Enhancers	Fetal Muscle Trunk	muscle
19	chr21:40168200-40170600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr21:40168200-40171000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr21:40168200-40171000	Enhancers	NH-A	brain
22	chr21:40168200-40171200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr21:40168400-40169800	Enhancers	K562	blood
24	chr21:40168400-40171800	Enhancers	HMEC	breast
25	chr21:40168400-40174000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr21:40168600-40170400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr21:40168600-40171200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr21:40168800-40170200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr21:40168800-40170600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr21:40168800-40172800	Enhancers	Stomach Mucosa	stomach
31	chr21:40168800-40174400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr21:40169000-40174200	Weak transcription	Fetal Lung	lung
33	chr21:40169200-40169800	Enhancers	Esophagus	oesophagus
34	chr21:40169200-40171200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr21:40169200-40171200	Enhancers	Placenta	Placenta
36	chr21:40169400-40169800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr21:40169400-40169800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr21:40169400-40169800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr21:40169400-40169800	Enhancers	NHLF	lung
40	chr21:40169400-40170000	Enhancers	HUVEC	blood vessel
41	chr21:40169400-40170200	Enhancers	Fetal Heart	heart
42	chr21:40169400-40170800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr21:40169400-40171000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr21:40169400-40171200	Flanking Active TSS	A549	lung
45	chr21:40169600-40169800	Flanking Active TSS	Hela-S3	cervix
46	chr21:40169600-40170200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr21:40169600-40170200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr21:40169600-40176800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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