Variant report

Variant	rs1209952
Chromosome Location	chr21:40175827-40175828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40175826-40184443	MCF10A-Er-Src	breast:	n/a	n/a
2	MAZ	chr21:40175795-40179353	IMR90	lung:	n/a	chr21:40176308-40176317 chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40176537-40176546 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
3	CHD1	chr21:40175807-40184420	IMR90	lung:	n/a	chr21:40183942-40183952
4	POLR2A	chr21:40175758-40179245	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
2	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
3	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
4	chr21:40174974..40176584-chr21:40544801..40546577,2	K562	blood:
5	chr21:40154093..40155752-chr21:40174948..40176789,2	MCF-7	breast:

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000272991	Chromatin interaction
ENSG00000234035	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1209930	0.83[ASN][1000 genomes]
rs1209932	0.83[CHB][hapmap]
rs1209935	0.80[CHB][hapmap]
rs1209943	0.81[CHB][hapmap]
rs1209944	0.82[CHD][hapmap]
rs1209949	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209951	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209954	0.85[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209955	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2070529	0.80[CEU][hapmap]
rs2070530	0.80[CEU][hapmap]
rs2156422	0.82[CHB][hapmap]
rs2256290	0.82[CHB][hapmap]
rs457705	0.87[CEU][hapmap]
rs460982	0.80[CEU][hapmap]
rs461155	0.87[CEU][hapmap]
rs9981039	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	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
3	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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40165000-40176600	Enhancers	Fetal Intestine Large	intestine
2	chr21:40166400-40176000	Weak transcription	Pancreas	Pancrea
3	chr21:40166600-40177000	Weak transcription	Gastric	stomach
4	chr21:40167000-40176600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr21:40169600-40176800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr21:40170400-40176600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr21:40170800-40176400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr21:40171200-40176600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:40171400-40176400	Weak transcription	Hela-S3	cervix
10	chr21:40171600-40176000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr21:40172000-40177000	Enhancers	HepG2	liver
12	chr21:40172600-40176800	Enhancers	K562	blood
13	chr21:40172600-40177200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr21:40173000-40176000	Weak transcription	Small Intestine	intestine
15	chr21:40173000-40176800	Weak transcription	Right Atrium	heart
16	chr21:40173400-40176800	Enhancers	Placenta	Placenta
17	chr21:40173600-40176800	Enhancers	Stomach Mucosa	stomach
18	chr21:40173800-40176600	Weak transcription	HMEC	breast
19	chr21:40174000-40176000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr21:40174000-40176200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr21:40174000-40176400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr21:40174000-40176400	Enhancers	Duodenum Mucosa	Duodenum
23	chr21:40174200-40176000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr21:40174200-40176600	Enhancers	Fetal Lung	lung
25	chr21:40174400-40176600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr21:40174400-40176800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr21:40174600-40176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:40175200-40176000	Enhancers	Colonic Mucosa	Colon
29	chr21:40175200-40176800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr21:40175400-40176200	Enhancers	Primary hematopoietic stem cells	blood
31	chr21:40175400-40176200	Genic enhancers	Fetal Intestine Small	intestine
32	chr21:40175400-40176200	Weak transcription	Osteobl	bone
33	chr21:40175400-40176600	Enhancers	NHEK	skin
34	chr21:40175400-40176800	Enhancers	Fetal Muscle Trunk	muscle
35	chr21:40175400-40176800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr21:40175400-40177000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:40175400-40177000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr21:40175400-40177000	Enhancers	Esophagus	oesophagus
39	chr21:40175400-40177200	Enhancers	Lung	lung
40	chr21:40175800-40176000	Flanking Active TSS	A549	lung
41	chr21:40175800-40176000	Enhancers	NHLF	lung
42	chr21:40175800-40176400	Enhancers	NH-A	brain
43	chr21:40175800-40176800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr21:40175800-40176800	Enhancers	Fetal Stomach	stomach

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