Variant report

Variant	rs1980909
Chromosome Location	chr1:153183327-153183328
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153182792..153185381-chr1:153188407..153191081,3	MCF-7	breast:
2	chr1:153182854..153185008-chr1:153187855..153189909,2	MCF-7	breast:
3	chr1:153180875..153183412-chr1:153183535..153185294,2	K562	blood:

Variant related genes	Relation type
ENSG00000203783	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11205236	0.93[ASN][1000 genomes]
rs12081567	0.93[ASN][1000 genomes]
rs12128109	0.93[ASN][1000 genomes]
rs12409595	0.93[ASN][1000 genomes]
rs12723408	0.93[ASN][1000 genomes]
rs12726323	0.93[ASN][1000 genomes]
rs12753856	0.93[ASN][1000 genomes]
rs1329098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1410858	0.97[ASN][1000 genomes]
rs1410862	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1831237	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34005908	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34846977	0.93[ASN][1000 genomes]
rs35713450	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55736513	0.93[ASN][1000 genomes]
rs6669600	0.93[ASN][1000 genomes]
rs6672400	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7514442	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7554353	0.97[ASN][1000 genomes]
rs943133	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1004168	chr1:153088209-153226033	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1013041	chr1:153105260-153223716	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1980909	NPR1	cis	cerebellum	SCAN
rs1980909	PGLYRP4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153182800-153183400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:153183000-153183400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:153183200-153205000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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