Variant report

Variant	rs56158137
Chromosome Location	chr1:152994380-152994381
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152994189..152995885-chr1:153004714..153007104,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169469	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10888528	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888529	0.92[EUR][1000 genomes]
rs1108410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11205179	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11205180	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205181	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11205182	0.93[EUR][1000 genomes]
rs11205185	0.82[AMR][1000 genomes]
rs11205186	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11205187	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11205188	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11205189	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11485498	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11488175	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11576797	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11590835	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11812015	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12079087	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12082627	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12083211	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1415972	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1500937	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1577960	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995308	0.98[EUR][1000 genomes]
rs28924721	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3737864	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4041402	0.84[AMR][1000 genomes]
rs41263664	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4845503	0.82[EUR][1000 genomes]
rs4845505	0.81[EUR][1000 genomes]
rs4845513	0.99[EUR][1000 genomes]
rs55906223	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56412380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61811886	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61811902	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61811903	0.92[EUR][1000 genomes]
rs61813181	0.82[AMR][1000 genomes]
rs61813182	0.84[AMR][1000 genomes]
rs6587724	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587725	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6660797	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6660878	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661059	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661063	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6664380	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6670380	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671520	0.84[AMR][1000 genomes]
rs6673356	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6675009	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6677674	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6680061	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6683514	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6686526	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6689066	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689510	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6692062	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6693927	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6698361	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7531076	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7532166	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7540609	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7543689	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7548977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551791	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv3416199	chr1:152957887-153005113	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	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
rs56158137	SPRR1B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152991600-152995600	Weak transcription	Esophagus	oesophagus
2	chr1:152994000-152994400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:152994000-152994400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:152994000-152994400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:152994000-152994600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:152994000-152994600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:152994200-153000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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