Variant report

Variant	rs2008672
Chromosome Location	chr15:56091864-56091865
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56090139..56092920-chr15:56116409..56118129,2	K562	blood:
2	chr15:56032752..56035214-chr15:56091096..56094057,2	MCF-7	breast:
3	chr15:55939872..55941462-chr15:56091567..56092720,22	MCF-7	breast:
4	chr14:77141813..77142316-chr15:56091817..56092480,2	MCF-7	breast:
5	chr15:55940259..55941893-chr15:56091674..56092667,4	K562	blood:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10518822	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11071219	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11635701	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11853766	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12439615	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12594225	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17238405	0.80[ASN][1000 genomes]
rs2014213	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414442	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28486084	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28673063	0.82[EUR][1000 genomes]
rs28807987	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34593948	0.84[ASN][1000 genomes]
rs4316693	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4395015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415961	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56179937	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs57692605	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57725406	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs59983763	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs60503643	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62046598	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7182436	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030099	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8030626	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8034279	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8034296	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8038986	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs933996	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2008672	PRTG	cis	Artery Aorta	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56089000-56093600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:56090600-56092600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:56090800-56092000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:56090800-56092600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr15:56091000-56092400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr15:56091000-56092400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr15:56091200-56092000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr15:56091400-56092000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:56091400-56092000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:56091400-56092000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr15:56091400-56092000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:56091400-56092400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:56091400-56092400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:56091400-56092400	Enhancers	Osteobl	bone
15	chr15:56091400-56092600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:56091400-56092600	Enhancers	Hela-S3	cervix
17	chr15:56091600-56092000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr15:56091600-56092000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:56091600-56092000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:56091600-56092000	Enhancers	Brain Anterior Caudate	brain
21	chr15:56091600-56092400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:56091600-56092400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:56091600-56092400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:56091800-56092000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:56091800-56092000	Flanking Active TSS	HepG2	liver
26	chr15:56091800-56092000	Enhancers	HSMM	muscle
27	chr15:56091800-56092000	Enhancers	HSMMtube	muscle
28	chr15:56091800-56092000	Enhancers	NHDF-Ad	bronchial
29	chr15:56091800-56094000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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