Variant report

Variant	rs7542827
Chromosome Location	chr1:120048472-120048473
allele	C/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	CTCF	chr1:120048463-120048507	GM13976	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120046437..120049249-chr1:120049394..120051111,2	MCF-7	breast:

Variant related genes	Relation type
HSD3B1	TF binding region
ENSG00000203857	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10157474	1.00[EUR][1000 genomes]
rs10494226	1.00[EUR][1000 genomes]
rs12405653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411048	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13376069	1.00[EUR][1000 genomes]
rs17023666	1.00[EUR][1000 genomes]
rs17023789	1.00[EUR][1000 genomes]
rs17023809	1.00[EUR][1000 genomes]
rs17023974	1.00[EUR][1000 genomes]
rs1856889	1.00[EUR][1000 genomes]
rs1977209	1.00[EUR][1000 genomes]
rs1998180	1.00[EUR][1000 genomes]
rs2208377	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2208378	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2273582	1.00[ASN][1000 genomes]
rs33937873	1.00[EUR][1000 genomes]
rs34035441	1.00[ASN][1000 genomes]
rs3765944	1.00[ASN][1000 genomes]
rs4258257	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4567318	1.00[EUR][1000 genomes]
rs56119175	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188766	1.00[EUR][1000 genomes]
rs56673765	1.00[EUR][1000 genomes]
rs56850733	1.00[EUR][1000 genomes]
rs56913763	1.00[EUR][1000 genomes]
rs57052489	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57583533	1.00[EUR][1000 genomes]
rs57803062	1.00[EUR][1000 genomes]
rs58233700	1.00[EUR][1000 genomes]
rs58428582	1.00[EUR][1000 genomes]
rs58575398	1.00[EUR][1000 genomes]
rs58689501	1.00[EUR][1000 genomes]
rs58933433	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59375730	1.00[EUR][1000 genomes]
rs59727458	1.00[EUR][1000 genomes]
rs59885501	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60417402	0.91[ASN][1000 genomes]
rs60438295	1.00[EUR][1000 genomes]
rs60498350	1.00[EUR][1000 genomes]
rs60502880	1.00[EUR][1000 genomes]
rs60876981	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60892766	0.91[ASN][1000 genomes]
rs61080896	1.00[EUR][1000 genomes]
rs61252879	0.91[ASN][1000 genomes]
rs61327356	1.00[ASN][1000 genomes]
rs61332695	1.00[EUR][1000 genomes]
rs61528123	1.00[EUR][1000 genomes]
rs6200	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6201	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6202	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6205	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6658109	1.00[EUR][1000 genomes]
rs6661258	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663113	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6670659	1.00[EUR][1000 genomes]
rs6670858	1.00[EUR][1000 genomes]
rs6671149	1.00[ASN][1000 genomes]
rs6673653	1.00[ASN][1000 genomes]
rs6674048	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674218	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6676283	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6685275	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688023	1.00[ASN][1000 genomes]
rs6690958	1.00[ASN][1000 genomes]
rs6691961	1.00[EUR][1000 genomes]
rs67392954	1.00[EUR][1000 genomes]
rs72561793	1.00[EUR][1000 genomes]
rs72986612	1.00[EUR][1000 genomes]
rs72986636	1.00[EUR][1000 genomes]
rs74114643	1.00[EUR][1000 genomes]
rs74114646	1.00[EUR][1000 genomes]
rs74114647	1.00[EUR][1000 genomes]
rs74114696	1.00[EUR][1000 genomes]
rs7517402	0.91[ASN][1000 genomes]
rs7519379	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7524638	1.00[ASN][1000 genomes]
rs7535128	1.00[EUR][1000 genomes]
rs7535899	1.00[EUR][1000 genomes]
rs876574	0.91[ASN][1000 genomes]
rs932603	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	38 gene(s)	inside rSNPs	diseases
8	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv524727	chr1:120023971-120056401	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120047400-120049800	Enhancers	Placenta	Placenta
2	chr1:120047800-120049600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:120047800-120050000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:120047800-120052200	Weak transcription	HMEC	breast
5	chr1:120048000-120051400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:120048000-120051600	Weak transcription	NHEK	skin
7	chr1:120048200-120051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:120048200-120052000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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