Variant report

Variant	rs28689606
Chromosome Location	chr1:153530231-153530232
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153529132..153532094-chr1:153535970..153538611,2	K562	blood:
2	chr1:153522864..153527279-chr1:153528529..153531164,4	K562	blood:
3	chr1:153507762..153509989-chr1:153530134..153533409,3	K562	blood:
4	chr1:153528658..153530749-chr1:153536638..153539695,4	MCF-7	breast:
5	chr1:153527411..153530387-chr1:153595127..153597966,2	MCF-7	breast:
6	chr1:153528403..153530464-chr1:153530665..153533438,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197956	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1047325	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050923	0.97[EUR][1000 genomes]
rs11488669	0.94[EUR][1000 genomes]
rs16835437	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835455	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452456	0.97[EUR][1000 genomes]
rs28548347	0.97[EUR][1000 genomes]
rs28594230	0.94[EUR][1000 genomes]
rs28718953	0.97[EUR][1000 genomes]
rs36022742	0.97[EUR][1000 genomes]
rs3762268	0.97[EUR][1000 genomes]
rs41265162	0.97[EUR][1000 genomes]
rs41265164	0.97[EUR][1000 genomes]
rs4595398	0.97[EUR][1000 genomes]
rs55955983	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043239	0.97[EUR][1000 genomes]
rs56057245	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089062	0.97[EUR][1000 genomes]
rs56350425	0.97[EUR][1000 genomes]
rs56838169	0.97[EUR][1000 genomes]
rs57024596	0.97[EUR][1000 genomes]
rs58056804	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58072118	0.97[EUR][1000 genomes]
rs59376279	0.97[EUR][1000 genomes]
rs60069797	1.00[ASN][1000 genomes]
rs60218214	0.97[EUR][1000 genomes]
rs60287468	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60969679	0.84[EUR][1000 genomes]
rs61265945	0.97[EUR][1000 genomes]
rs61558997	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427301	0.97[EUR][1000 genomes]
rs6671398	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700310	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6702891	1.00[ASN][1000 genomes]
rs6703014	1.00[ASN][1000 genomes]
rs73026350	0.97[EUR][1000 genomes]
rs74115473	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74115476	0.94[EUR][1000 genomes]
rs7535476	0.81[EUR][1000 genomes]
rs8401	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
4	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153522600-153538000	Weak transcription	Colonic Mucosa	Colon
2	chr1:153526600-153534000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:153527200-153536200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:153527200-153536400	Weak transcription	Spleen	Spleen
5	chr1:153527400-153531400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:153527400-153534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:153527400-153535800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:153527400-153536200	Weak transcription	NHLF	lung
9	chr1:153527600-153530400	Strong transcription	NHEK	skin
10	chr1:153527600-153530600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:153527600-153532800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:153527600-153535200	Weak transcription	Esophagus	oesophagus
13	chr1:153527600-153536000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:153527600-153536200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:153529400-153530400	Strong transcription	HMEC	breast
16	chr1:153529400-153534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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