Variant report

Variant	rs57740627
Chromosome Location	chr21:40180659-40180660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

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	POLR2A	chr21:40177100-40180919	PBDE	blood:	n/a	n/a
3	POLR2A	chr21:40179677-40180934	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr21:40179647-40183609	HepG2	liver:	n/a	n/a
5	POLR2A	chr21:40179551-40187734	A549	lung:	n/a	n/a
6	POLR2A	chr21:40175924-40187316	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr21:40179759-40180941	HepG2	liver:	n/a	n/a
8	POLR2A	chr21:40180496-40180827	K562	blood:	n/a	n/a
9	POLR2A	chr21:40179258-40183612	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr21:40179887-40180804	Hela-S3	cervix:	n/a	n/a
11	CHD1	chr21:40175807-40184420	IMR90	lung:	n/a	chr21:40183942-40183952
12	POLR2A	chr21:40179313-40180958	HepG2	liver:	n/a	n/a
13	POLR2A	chr21:40179797-40181024	HepG2	liver:	n/a	n/a
14	POLR2A	chr21:40178590-40182958	HepG2	liver:	n/a	n/a
15	CEBPB	chr21:40180634-40180815	HepG2	liver:	n/a	n/a
16	POLR2A	chr21:40176463-40183519	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr21:40176087-40184309	IMR90	lung:	n/a	n/a
18	POLR2A	chr21:40179569-40181001	HL-60	blood:	n/a	n/a
19	POLR2A	chr21:40176373-40183421	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56708960..56710551-chr21:40179087..40181120,2	MCF-7	breast:
2	chr21:40110884..40114912-chr21:40179006..40181984,4	MCF-7	breast:
3	chr21:40178699..40181140-chr21:40363859..40366639,2	MCF-7	breast:
4	chr21:40084560..40086219-chr21:40178375..40180682,2	MCF-7	breast:
5	chr21:40179587..40181228-chr21:40445406..40447248,2	MCF-7	breast:

No data

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000223806	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11701301	0.81[ASN][1000 genomes]
rs11911369	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17230954	0.85[ASN][1000 genomes]
rs17230961	0.85[ASN][1000 genomes]
rs2298560	0.89[ASN][1000 genomes]
rs2410062	0.85[ASN][1000 genomes]
rs2836715	0.81[ASN][1000 genomes]
rs2836717	0.81[ASN][1000 genomes]
rs2836720	0.81[ASN][1000 genomes]
rs2836724	0.81[ASN][1000 genomes]
rs28375993	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28508188	0.81[ASN][1000 genomes]
rs28817686	0.81[ASN][1000 genomes]
rs28836833	0.81[ASN][1000 genomes]
rs467698	0.81[ASN][1000 genomes]
rs467806	0.81[ASN][1000 genomes]
rs59086904	0.81[ASN][1000 genomes]
rs60328145	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs714780	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7278693	0.85[ASN][1000 genomes]
rs7279299	0.85[ASN][1000 genomes]
rs7283433	0.85[ASN][1000 genomes]
rs73450548	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450552	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128181	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133056	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133164	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134019	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134441	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40176600-40181600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr21:40176600-40182000	Active TSS	Brain Anterior Caudate	brain
3	chr21:40176800-40181000	Active TSS	Brain Angular Gyrus	brain
4	chr21:40176800-40182800	Active TSS	Brain Cingulate Gyrus	brain
5	chr21:40176800-40182800	Active TSS	Brain Hippocampus Middle	brain
6	chr21:40177000-40181400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr21:40177200-40182400	Active TSS	Lung	lung
8	chr21:40177600-40182200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr21:40178600-40182800	Transcr. at gene 5' and 3'	NHEK	skin
10	chr21:40178800-40181600	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr21:40179000-40180800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr21:40179000-40182800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
13	chr21:40179000-40184000	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr21:40179000-40184800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr21:40179200-40180800	Enhancers	Fetal Heart	heart
16	chr21:40179200-40181800	Weak transcription	HSMM	muscle
17	chr21:40179200-40184600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr21:40179400-40181000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr21:40179400-40181000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr21:40179400-40181600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr21:40179400-40182000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr21:40179600-40180800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr21:40179600-40181000	Flanking Active TSS	HMEC	breast
24	chr21:40179600-40181800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr21:40179600-40181800	Transcr. at gene 5' and 3'	HepG2	liver
26	chr21:40179600-40182200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr21:40179600-40182400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr21:40179600-40182600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
29	chr21:40179600-40182600	Weak transcription	Osteobl	bone
30	chr21:40179600-40183000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr21:40179600-40183600	Transcr. at gene 5' and 3'	A549	lung
32	chr21:40179600-40184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr21:40179600-40184800	Weak transcription	HSMMtube	muscle
34	chr21:40179800-40181400	Genic enhancers	K562	blood
35	chr21:40179800-40181600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
36	chr21:40179800-40181800	Transcr. at gene 5' and 3'	Fetal Lung	lung
37	chr21:40179800-40182800	Transcr. at gene 5' and 3'	Hela-S3	cervix
38	chr21:40179800-40183000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr21:40179800-40183400	Transcr. at gene 5' and 3'	Liver	Liver
40	chr21:40179800-40185200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr21:40180000-40180800	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr21:40180000-40181000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr21:40180000-40181000	Enhancers	Stomach Mucosa	stomach
44	chr21:40180000-40181200	Weak transcription	Primary T cells from cord blood	blood
45	chr21:40180000-40181600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr21:40180000-40181600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
47	chr21:40180000-40181800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr21:40180000-40181800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr21:40180000-40182200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
50	chr21:40180000-40182800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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