Variant report

Variant	rs9941892
Chromosome Location	chr21:40211235-40211236
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40207571..40212513-chr21:40281866..40285274,6	MCF-7	breast:
2	chr21:40203275..40206794-chr21:40210041..40212530,5	MCF-7	breast:
3	chr21:40176595..40179182-chr21:40208823..40211776,3	K562	blood:
4	chr21:40175934..40178688-chr21:40209789..40212200,2	MCF-7	breast:
5	chr21:40205616..40208986-chr21:40210258..40212560,3	MCF-7	breast:
6	chr21:40206775..40209110-chr21:40210646..40213517,2	K562	blood:
7	chr21:40210912..40213065-chr21:40219265..40221347,3	K562	blood:
8	chr21:40209144..40212226-chr21:40213678..40216387,3	K562	blood:
9	chr21:40209378..40211862-chr21:40284823..40286804,2	MCF-7	breast:
10	chr21:40209482..40212563-chr21:40213470..40216289,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1000844	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1009121	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051475	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051476	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10854389	0.84[ASN][1000 genomes]
rs11088449	0.80[CEU][hapmap]
rs11088450	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11088451	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11088452	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11088453	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11088454	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1123350	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11701191	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11701500	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs11702403	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12481740	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12482470	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12483746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12627283	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13046853	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13047133	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13047537	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13047745	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13048035	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13050340	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571707	0.94[CHB][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070531	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142035	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836683	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836684	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836685	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836686	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836687	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836688	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836689	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836690	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836691	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836692	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836693	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836694	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836710	0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836711	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517481	0.86[EUR][1000 genomes]
rs7276961	0.85[EUR][1000 genomes]
rs7282444	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7282723	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs762387	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs998855	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9941892	ETS2	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
2	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
3	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
4	chr21:40197000-40211800	Weak transcription	Esophagus	oesophagus
5	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
6	chr21:40205400-40211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:40209800-40212200	Enhancers	HepG2	liver
8	chr21:40209800-40212200	Enhancers	HUVEC	blood vessel
9	chr21:40210000-40211400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:40210000-40212200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr21:40210000-40212400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr21:40210000-40212800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr21:40210000-40214000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:40210000-40214000	Enhancers	NHEK	skin
15	chr21:40210000-40214200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr21:40210000-40214200	Enhancers	HMEC	breast
17	chr21:40210200-40211800	Weak transcription	Placenta	Placenta
18	chr21:40210200-40212200	Enhancers	Fetal Muscle Trunk	muscle
19	chr21:40210200-40212400	Enhancers	NHLF	lung
20	chr21:40210200-40212800	Enhancers	NHDF-Ad	bronchial
21	chr21:40210200-40213800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:40210400-40212400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr21:40210400-40212400	Enhancers	HSMM	muscle
24	chr21:40210400-40212600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr21:40210400-40212800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr21:40210600-40212000	Enhancers	Fetal Stomach	stomach
27	chr21:40210600-40212200	Enhancers	HSMMtube	muscle
28	chr21:40210800-40211400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:40210800-40211800	Enhancers	NH-A	brain
30	chr21:40210800-40212000	Enhancers	Small Intestine	intestine
31	chr21:40210800-40212400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr21:40211000-40212200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr21:40211000-40212200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr21:40211000-40212200	Enhancers	Fetal Muscle Leg	muscle
35	chr21:40211000-40212200	Flanking Active TSS	Osteobl	bone
36	chr21:40211200-40211600	Enhancers	Fetal Intestine Large	intestine
37	chr21:40211200-40211800	Active TSS	A549	lung
38	chr21:40211200-40211800	Enhancers	Hela-S3	cervix
39	chr21:40211200-40212000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr21:40211200-40212200	Enhancers	K562	blood

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