Variant report

Variant	rs4571672
Chromosome Location	chr7:100710389-100710390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100491120..100492820-chr7:100709572..100712044,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087085	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10229731	1.00[CEU][hapmap]
rs10231438	0.81[CHB][hapmap]
rs10231529	0.81[CHB][hapmap]
rs10242132	1.00[CEU][hapmap]
rs10259584	1.00[CEU][hapmap]
rs10953318	0.81[CHB][hapmap]
rs10953321	0.84[TSI][hapmap]
rs10953322	0.80[TSI][hapmap]
rs11772356	0.93[CHB][hapmap]
rs11972491	0.80[TSI][hapmap]
rs12667943	0.93[CHB][hapmap]
rs12668231	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13221804	0.90[CEU][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13225064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13228919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232139	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13235999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239478	1.00[CEU][hapmap]
rs2227672	0.81[CHB][hapmap]
rs2227690	0.86[CHB][hapmap]
rs28651567	0.83[EUR][1000 genomes]
rs34411816	0.82[EUR][1000 genomes]
rs35723463	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35783870	0.82[EUR][1000 genomes]
rs35802441	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35988443	0.82[EUR][1000 genomes]
rs4269454	1.00[CEU][hapmap]
rs4422700	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4613910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729644	1.00[CEU][hapmap]
rs6092	0.81[CHB][hapmap]
rs73168398	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73170203	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73178503	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73178506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73178512	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7786422	0.84[EUR][1000 genomes]
rs9791379	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9791726	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9792109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv1826021	chr7:100525848-100749246	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1846644	chr7:100525848-100749246	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1822460	chr7:100606044-100749246	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv427796	chr7:100606044-100749246	Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv428181	chr7:100606044-100749246	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv831074	chr7:100606051-100745532	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1033081	chr7:100669629-100771824	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	esv1811048	chr7:100675933-100730280	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1831657	chr7:100675933-100730280	Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
16	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4571672	TRRAP	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100709200-100710400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:100709200-100710400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr7:100709400-100710400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr7:100709400-100710400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr7:100709400-100710400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:100709400-100710400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:100709400-100710400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr7:100709400-100710400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr7:100709400-100710400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:100709400-100710400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:100709400-100710400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:100709400-100710400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr7:100709400-100710600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:100709400-100710600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:100709600-100710400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:100709600-100710400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:100710000-100710400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:100710000-100710600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:100710200-100710400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr7:100710200-100710400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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