Variant report

Variant	rs3915524
Chromosome Location	chr1:153476901-153476902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:153476710-153476911	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:153476734-153476909	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:153476647-153477038	MCF-7	breast:	n/a	n/a
4	CTCF	chr1:153476726-153476912	MCF-7	breast:	n/a	n/a
5	RAD21	chr1:153476632-153477070	MCF-7	breast:	n/a	n/a
6	RAD21	chr1:153476634-153476936	MCF-7	breast:	n/a	n/a
7	CTCF	chr1:153476725-153476904	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:153476840-153476990	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:153476721-153476910	MCF-7	breast:	n/a	n/a
10	RAD21	chr1:153476639-153476938	A549	lung:	n/a	n/a
11	CTCF	chr1:153476662-153476930	MCF-7	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153475901..153479398-chr1:153483925..153488105,4	K562	blood:
2	chr1:153325822..153326705-chr1:153475963..153477276,5	MCF-7	breast:
3	chr1:153476869..153479043-chr1:153480773..153483334,2	K562	blood:
4	chr1:153474662..153477401-chr1:153483701..153485425,2	K562	blood:
5	chr1:153327773..153328466-chr1:153476559..153477244,2	MCF-7	breast:
6	chr1:153468303..153470815-chr1:153474677..153477799,3	K562	blood:
7	chr1:153324272..153325645-chr1:153476051..153477089,5	MCF-7	breast:
8	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
9	chr1:153326072..153327690-chr1:153475261..153477527,2	MCF-7	breast:
10	chr1:153475147..153477095-chr1:153963171..153964813,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL44P	TF binding region
ENSG00000177954	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction

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

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

rs_ID	r²[population]
rs16835366	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835368	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835382	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835393	0.85[ASN][1000 genomes]
rs17695220	0.88[ASN][1000 genomes]
rs1887039	0.85[ASN][1000 genomes]
rs1964151	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339696	0.88[ASN][1000 genomes]
rs28410699	0.88[ASN][1000 genomes]
rs28464843	0.88[ASN][1000 genomes]
rs28632016	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28635377	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28676601	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28707433	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845548	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845549	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845550	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845551	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845552	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845553	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845554	0.85[ASN][1000 genomes]
rs6587743	0.88[ASN][1000 genomes]
rs6587745	0.88[ASN][1000 genomes]
rs6587746	0.88[ASN][1000 genomes]
rs6660055	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6672390	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6679509	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6690638	0.85[ASN][1000 genomes]
rs6690712	0.85[ASN][1000 genomes]
rs6696893	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515940	0.85[ASN][1000 genomes]
rs7520093	0.88[ASN][1000 genomes]
rs7534343	0.86[ASN][1000 genomes]
rs7534347	0.88[ASN][1000 genomes]
rs7534830	0.85[ASN][1000 genomes]
rs7537898	0.85[ASN][1000 genomes]
rs7544359	0.85[ASN][1000 genomes]
rs9436094	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9436095	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	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
5	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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
2	chr1:153467200-153478000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:153468400-153479000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153471800-153477800	Weak transcription	Ovary	ovary
5	chr1:153471800-153478800	Weak transcription	Fetal Stomach	stomach
6	chr1:153472400-153478200	Weak transcription	Aorta	Aorta
7	chr1:153474400-153478400	Weak transcription	Fetal Lung	lung
8	chr1:153475400-153478800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:153476000-153478000	Weak transcription	HSMM	muscle
10	chr1:153476400-153477800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:153476600-153478800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:153476800-153477000	Enhancers	HMEC	breast
13	chr1:153476800-153477200	Enhancers	NHEK	skin

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