Variant report

Variant	rs209969
Chromosome Location	chr20:52732711-52732712
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56735269..56738052-chr20:52731872..52734487,3	MCF-7	breast:
2	chr20:52731963..52732914-chr20:52765695..52766299,2	MCF-7	breast:
3	chr17:56734883..56738344-chr20:52732166..52735688,4	MCF-7	breast:
4	chr17:56755556..56757085-chr20:52731097..52733243,2	MCF-7	breast:
5	chr20:52730207..52733143-chr6:154815042..154816993,2	MCF-7	breast:
6	chr17:56704127..56711907-chr20:52729106..52752952,70	MCF-7	breast:
7	chr17:57183456..57185840-chr20:52732574..52734968,2	MCF-7	breast:
8	chr20:52728274..52735407-chr20:55838077..55845201,12	MCF-7	breast:
9	chr17:56706370..56714481-chr20:52725604..52746501,43	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224738	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2585444	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2762917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs209969	IL1R1	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52725000-52740200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:52728200-52737600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:52729000-52733000	Enhancers	Fetal Intestine Large	intestine
4	chr20:52730800-52733400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr20:52730800-52738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr20:52731000-52733000	Enhancers	Colonic Mucosa	Colon
7	chr20:52731400-52733000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr20:52731400-52733000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:52731600-52733000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:52731600-52733000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:52731600-52733200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr20:52731800-52733000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52731800-52733000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:52731800-52733000	Enhancers	Lung	lung
15	chr20:52731800-52733400	Enhancers	Liver	Liver
16	chr20:52732000-52739400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:52732200-52733200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr20:52732200-52739400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:52732400-52733200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr20:52732400-52733800	Weak transcription	NHEK	skin
21	chr20:52732400-52735000	Enhancers	A549	lung
22	chr20:52732400-52735000	Weak transcription	HMEC	breast
23	chr20:52732400-52738200	Weak transcription	NHDF-Ad	bronchial
24	chr20:52732400-52738200	Weak transcription	Osteobl	bone
25	chr20:52732400-52738800	Enhancers	HepG2	liver
26	chr20:52732600-52733400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr20:52732600-52733800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr20:52732600-52738000	Weak transcription	Hela-S3	cervix

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