Variant report

Variant	rs12090961
Chromosome Location	chr1:159768539-159768540
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	RAD21	chr1:159768525-159769174	A549	lung:	n/a	chr1:159768780-159768799
2	RAD21	chr1:159768531-159769072	MCF-7	breast:	n/a	chr1:159768780-159768799
3	CTCF	chr1:159768331-159769406	HCT-116	colon:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
4	MAX	chr1:159768526-159769174	A549	lung:	n/a	n/a
5	CTCF	chr1:159768506-159769213	MCF-7	breast:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
6	RAD21	chr1:159768423-159769414	SK-N-SH	brain:	n/a	chr1:159768780-159768799
7	RAD21	chr1:159768509-159769122	IMR90	lung:	n/a	chr1:159768780-159768799
8	CBX3	chr1:159768487-159769320	HCT-116	colon:	n/a	n/a
9	CTCF	chr1:159768509-159769188	A549	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
10	RAD21	chr1:159768528-159769086	H1-hESC	embryonic stem cell:	n/a	chr1:159768780-159768799
11	CTCF	chr1:159768395-159769219	HCT-116	colon:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
12	RAD21	chr1:159768358-159769319	HCT-116	colon:	n/a	chr1:159768780-159768799
13	GATA3	chr1:159768270-159768574	SH-SY5Y	brain:	n/a	n/a
14	RAD21	chr1:159768407-159769270	HCT-116	colon:	n/a	chr1:159768780-159768799
15	RAD21	chr1:159768537-159769142	ECC-1	luminal epithelium:	n/a	chr1:159768780-159768799
16	SMC3	chr1:159768492-159769355	SK-N-SH	brain:	n/a	chr1:159768781-159768795
17	CTCF	chr1:159768524-159769024	HepG2	liver:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
18	CTCF	chr1:159768192-159769475	A549	lung:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
19	CTCF	chr1:159768236-159769530	SK-N-SH	brain:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
20	CTCF	chr1:159768539-159769158	MCF-7	breast:	n/a	chr1:159768780-159768796 chr1:159768922-159768940 chr1:159768781-159768802 chr1:159768779-159768797
21	RAD21	chr1:159768437-159769185	A549	lung:	n/a	chr1:159768780-159768799
22	CUX1	chr1:159768536-159768991	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:159767764..159770005-chr1:159860953..159862581,56	MCF-7	breast:
2	chr1:159767618..159769808-chr1:159861062..159862249,21	MCF-7	breast:
3	chr1:159768345..159769282-chr1:159859526..159860741,4	MCF-7	breast:
4	chr1:159768315..159769250-chr1:159861096..159861662,3	K562	blood:
5	chr1:159767829..159770101-chr1:159851843..159854552,2	MCF-7	breast:
6	chr1:159768046..159769566-chr1:159975811..159977855,12	K562	blood:
7	chr1:159768235..159769330-chr1:159915062..159916235,4	K562	blood:
8	chr1:159756652..159760361-chr1:159765566..159768582,3	K562	blood:
9	chr1:159768310..159769697-chr1:159798745..159799727,11	MCF-7	breast:
10	chr1:159767920..159768832-chr1:159977164..159978145,2	MCF-7	breast:
11	chr1:159767187..159770392-chr1:159770720..159774821,3	K562	blood:
12	chr1:159760951..159764398-chr1:159766034..159769710,4	K562	blood:
13	chr1:159766964..159768687-chr1:159770720..159772880,2	K562	blood:

Variant related genes	Relation type
FCRL6	TF binding region
ENSG00000181036	Chromatin interaction
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11265280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265282	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585836	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11590961	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12083967	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4301626	1.00[JPT][hapmap]
rs4443889	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4656851	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55650803	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57198275	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58024147	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58240276	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59414252	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656168	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656979	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6657365	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6659704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672434	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7512164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527418	0.86[CEU][hapmap]

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	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv521503	chr1:159762120-159795478	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159765600-159770000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:159768400-159771400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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