Variant report

Variant	rs2009227
Chromosome Location	chr17:53523340-53523341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:53522618..53523529-chr7:107502421..107503000,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLF-3	chr17:53523226-53523576	expReg_chr17_9179_+

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11870717	0.83[EUR][1000 genomes]
rs12451745	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12944990	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35686442	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794592	0.83[EUR][1000 genomes]
rs7220600	0.83[EUR][1000 genomes]
rs9303370	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9890254	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9890288	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9899752	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903218	0.82[EUR][1000 genomes]
rs9910434	0.82[EUR][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	nsv2100	chr17:53492380-54328516	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1062337	chr17:53510996-54161442	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:53499400-53528000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:53517600-53524400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:53519000-53523800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr17:53520200-53523600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr17:53520400-53524200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:53520600-53524600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:53521000-53524400	Enhancers	Colon Smooth Muscle	Colon
8	chr17:53521400-53524600	Enhancers	Small Intestine	intestine
9	chr17:53522200-53524000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr17:53522200-53525200	Enhancers	Liver	Liver
11	chr17:53522400-53525800	Weak transcription	Placenta	Placenta
12	chr17:53522400-53527800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr17:53522600-53523600	Weak transcription	Hela-S3	cervix
14	chr17:53522600-53524000	Weak transcription	Fetal Lung	lung
15	chr17:53522600-53525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:53522600-53527000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:53522600-53529600	Weak transcription	HMEC	breast
18	chr17:53522800-53523600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr17:53522800-53523800	Weak transcription	Adipose Nuclei	Adipose
20	chr17:53522800-53524000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr17:53522800-53524000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:53522800-53524000	Enhancers	A549	lung
23	chr17:53522800-53525800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:53522800-53526000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr17:53522800-53526000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:53522800-53526000	Weak transcription	K562	blood
27	chr17:53522800-53526000	Weak transcription	Osteobl	bone
28	chr17:53522800-53526200	Weak transcription	NHLF	lung
29	chr17:53522800-53526800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:53522800-53529600	Weak transcription	NH-A	brain
31	chr17:53522800-53531200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr17:53523000-53523400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr17:53523000-53523400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:53523000-53523600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:53523000-53523800	Weak transcription	Fetal Intestine Small	intestine
36	chr17:53523000-53524000	Weak transcription	Fetal Intestine Large	intestine
37	chr17:53523000-53528000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:53523200-53523600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:53523200-53523600	Enhancers	HepG2	liver
40	chr17:53523200-53524000	Weak transcription	GM12878-XiMat	blood
41	chr17:53523200-53526000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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