Variant report

Variant	rs8401
Chromosome Location	chr1:153533898-153533899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153532385..153534203-chr1:153962213..153964792,2	K562	blood:
2	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
3	chr1:153532321..153535905-chr1:153536824..153539528,6	MCF-7	breast:
4	chr1:153505356..153506611-chr1:153533554..153534092,3	MCF-7	breast:
5	chr1:153531601..153533960-chr1:153598584..153600144,2	MCF-7	breast:
6	chr1:153513559..153517325-chr1:153533202..153535320,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189171	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000238279	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1047325	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050923	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs11488669	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16835437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810765	0.89[CEU][hapmap]
rs28452456	0.88[EUR][1000 genomes]
rs28548347	0.88[EUR][1000 genomes]
rs28594230	0.91[EUR][1000 genomes]
rs28689606	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718953	0.88[EUR][1000 genomes]
rs36022742	0.88[EUR][1000 genomes]
rs3762268	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs41265162	0.88[EUR][1000 genomes]
rs41265164	0.88[EUR][1000 genomes]
rs4595398	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs55955983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043239	0.88[EUR][1000 genomes]
rs56057245	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089062	0.88[EUR][1000 genomes]
rs56350425	0.88[EUR][1000 genomes]
rs56838169	0.88[EUR][1000 genomes]
rs57024596	0.88[EUR][1000 genomes]
rs58056804	0.91[EUR][1000 genomes]
rs58072118	0.88[EUR][1000 genomes]
rs59376279	0.88[EUR][1000 genomes]
rs60069797	1.00[ASN][1000 genomes]
rs60218214	0.94[EUR][1000 genomes]
rs60287468	0.91[EUR][1000 genomes]
rs61265945	0.88[EUR][1000 genomes]
rs61558997	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427301	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6671398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700310	0.85[EUR][1000 genomes]
rs6702891	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6703014	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73026350	0.88[EUR][1000 genomes]
rs74115473	0.91[EUR][1000 genomes]
rs74115476	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8401	S100A3	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 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	chr1:153527400-153534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:153527400-153535800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:153527400-153536200	Weak transcription	NHLF	lung
8	chr1:153527600-153535200	Weak transcription	Esophagus	oesophagus
9	chr1:153527600-153536000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:153527600-153536200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:153529400-153534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:153532800-153534000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:153532800-153539600	Weak transcription	Thymus	Thymus
14	chr1:153533200-153534000	Enhancers	Fetal Lung	lung
15	chr1:153533200-153534400	Enhancers	Ovary	ovary
16	chr1:153533600-153534200	Genic enhancers	NHEK	skin
17	chr1:153533800-153534400	Enhancers	A549	lung
18	chr1:153533800-153537400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:153533800-153537400	Transcr. at gene 5' and 3'	HMEC	breast
20	chr1:153533800-153537600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin

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