Variant report

Variant	rs35242257
Chromosome Location	chr6:54709391-54709392
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:54709178-54709446	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:54709139..54711220-chr6:54750997..54752618,2	MCF-7	breast:
2	chr20:52738859..52741782-chr6:54708785..54710307,2	MCF-7	breast:
3	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
4	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224984	TF binding region
FAM83B	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12196439	1.00[ASN][1000 genomes]
rs12207828	1.00[ASN][1000 genomes]
rs13190743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192654	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212537	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13218354	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13220607	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395638	1.00[ASN][1000 genomes]
rs1395639	1.00[ASN][1000 genomes]
rs17682062	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239782	1.00[ASN][1000 genomes]
rs239784	1.00[ASN][1000 genomes]
rs239785	1.00[ASN][1000 genomes]
rs34317450	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784567	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35332422	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355591	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35601036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776136	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929628	1.00[ASN][1000 genomes]
rs6930882	1.00[ASN][1000 genomes]
rs6936719	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560861	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560863	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560865	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560870	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560871	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560872	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9464152	1.00[ASN][1000 genomes]
rs9474993	1.00[ASN][1000 genomes]
rs9474994	1.00[ASN][1000 genomes]
rs9474998	1.00[ASN][1000 genomes]
rs9474999	1.00[ASN][1000 genomes]
rs9475000	1.00[ASN][1000 genomes]
rs9475047	1.00[ASN][1000 genomes]
rs9475049	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54707200-54710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:54707400-54710200	Weak transcription	NHEK	skin
3	chr6:54707400-54710800	Weak transcription	Placenta	Placenta
4	chr6:54709000-54709400	Enhancers	Fetal Intestine Small	intestine
5	chr6:54709000-54710000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:54709000-54710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
9	chr6:54709200-54709800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:54709200-54710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:54709200-54710200	Enhancers	HMEC	breast

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