Variant report

Variant	rs28489441
Chromosome Location	chr17:17346559-17346560
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17345336..17348353-chr17:17348575..17352300,3	K562	blood:
2	chr17:17345875..17348341-chr17:17739755..17742747,2	MCF-7	breast:
3	chr17:17346012..17348708-chr17:17349032..17351296,2	MCF-7	breast:
4	chr17:17344282..17356772-chr17:17394630..17405312,31	MCF-7	breast:
5	chr17:17340093..17354118-chr17:17394085..17402192,31	MCF-7	breast:
6	chr17:17344606..17346836-chr17:17348575..17350374,2	K562	blood:

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1123297	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11650117	0.86[ASN][1000 genomes]
rs11654572	0.91[ASN][1000 genomes]
rs12449517	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453750	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925141	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6502596	0.89[ASN][1000 genomes]
rs7216896	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7501994	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs925095	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058849	chr17:17308009-17348548	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1058804	chr17:17308984-17348548	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv574523	chr17:17310886-17347995	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1056137	chr17:17311017-17348939	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv543235	chr17:17311017-17348939	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17330200-17350000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:17335400-17348800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:17339200-17346800	Weak transcription	Thymus	Thymus
4	chr17:17339600-17347000	Weak transcription	HUVEC	blood vessel
5	chr17:17341400-17346600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:17344000-17348400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:17344000-17348600	Weak transcription	Gastric	stomach
8	chr17:17344000-17348800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:17344000-17348800	Weak transcription	Fetal Heart	heart
10	chr17:17344000-17349000	Weak transcription	Right Atrium	heart
11	chr17:17344000-17350000	Weak transcription	Dnd41	blood
12	chr17:17344200-17346600	Weak transcription	Liver	Liver
13	chr17:17344200-17348400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:17344200-17348600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:17344600-17347000	Weak transcription	Spleen	Spleen
16	chr17:17344600-17348600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:17344800-17346600	Weak transcription	Hela-S3	cervix
18	chr17:17344800-17347000	Weak transcription	Pancreas	Pancrea
19	chr17:17344800-17348400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:17344800-17348600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr17:17344800-17348600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:17344800-17348600	Weak transcription	Fetal Muscle Leg	muscle
23	chr17:17344800-17348800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:17344800-17348800	Weak transcription	NHDF-Ad	bronchial
25	chr17:17344800-17349000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr17:17344800-17349000	Weak transcription	Left Ventricle	heart
27	chr17:17344800-17353400	Weak transcription	Brain Germinal Matrix	brain
28	chr17:17345000-17346600	Weak transcription	Fetal Thymus	thymus
29	chr17:17345000-17346600	Weak transcription	HepG2	liver
30	chr17:17345000-17348400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:17345800-17346800	Weak transcription	Lung	lung
32	chr17:17346200-17348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr17:17346400-17347000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:17346400-17347200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:17346400-17348600	Enhancers	A549	lung

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