Variant report

Variant	rs4320779
Chromosome Location	chr1:152626540-152626541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr1:152626509-152626684	K562	blood:	n/a	n/a
2	SMC3	chr1:152626234-152626882	GM12878	blood:	n/a	n/a
3	CTCF	chr1:152626538-152626835	Medullo	brain:	n/a	n/a
4	CTCF	chr1:152626526-152626786	ProgFib	skin:	n/a	n/a
5	CTCF	chr1:152626517-152626817	LNCaP	prostate:	n/a	n/a
6	RAD21	chr1:152626511-152626942	MCF-7	breast:	n/a	n/a
7	RAD21	chr1:152626498-152626889	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr1:152626498-152626906	GM12878	blood:	n/a	n/a
9	CTCF	chr1:152626340-152627054	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr1:152626521-152626805	MCF-7	breast:	n/a	n/a
11	RAD21	chr1:152626534-152626930	HepG2	liver:	n/a	n/a
12	ZNF143	chr1:152626484-152626830	K562	blood:	n/a	n/a
13	CTCF	chr1:152626525-152626792	GM12892	blood:	n/a	n/a
14	RAD21	chr1:152626420-152626799	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr1:152626506-152626826	SK-N-SH_RA	brain:	n/a	n/a
16	RAD21	chr1:152626499-152626889	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr1:152626401-152626993	MCF-7	breast:	n/a	n/a
18	ZNF143	chr1:152626531-152626837	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr1:152626479-152626999	K562	blood:	n/a	n/a
20	CTCF	chr1:152626529-152626784	NHEK	skin:	n/a	n/a
21	RAD21	chr1:152626450-152626941	ECC-1	luminal epithelium:	n/a	n/a
22	MYC	chr1:152626457-152626727	MCF10A-Er-Src	breast:	n/a	n/a
23	ZNF143	chr1:152626532-152626813	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr1:152626441-152626919	A549	lung:	n/a	n/a
25	FOS	chr1:152626527-152626726	MCF10A-Er-Src	breast:	n/a	n/a
26	SMC3	chr1:152626479-152626864	K562	blood:	n/a	n/a
27	CTCF	chr1:152626049-152627081	A549	lung:	n/a	n/a
28	CTCF	chr1:152626516-152626803	GM19238	blood:	n/a	n/a
29	CTCF	chr1:152626440-152626590	HCM	heart:	n/a	n/a
30	CTCF	chr1:152626528-152626809	GM12878	blood:	n/a	n/a
31	ZNF384	chr1:152626520-152626925	GM12878	blood:	n/a	n/a
32	MAZ	chr1:152626514-152626832	K562	blood:	n/a	n/a
33	RAD21	chr1:152626521-152626816	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr1:152626444-152626899	A549	lung:	n/a	n/a
35	CTCF	chr1:152626504-152626877	K562	blood:	n/a	n/a
36	CTCF	chr1:152626461-152626839	HepG2	liver:	n/a	n/a
37	SMC3	chr1:152626492-152626855	HepG2	liver:	n/a	n/a
38	ZNF143	chr1:152626504-152626868	GM12878	blood:	n/a	n/a
39	MYC	chr1:152626526-152626726	K562	blood:	n/a	n/a
40	CTCF	chr1:152626514-152626845	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr1:152626431-152626960	MCF-7	breast:	n/a	n/a
42	CTCF	chr1:152626386-152626986	HCT-116	colon:	n/a	n/a
43	RAD21	chr1:152626493-152626871	HepG2	liver:	n/a	n/a
44	CTCF	chr1:152626533-152626810	K562	blood:	n/a	n/a
45	MXI1	chr1:152626533-152626675	HepG2	liver:	n/a	n/a
46	CTCF	chr1:152626532-152626815	GM13977	blood:	n/a	n/a
47	CTCF	chr1:152626405-152627028	HCT-116	colon:	n/a	n/a
48	RAD21	chr1:152626515-152626855	HepG2	liver:	n/a	n/a
49	ZNF384	chr1:152626507-152627002	K562	blood:	n/a	n/a
50	CTCF	chr1:152626540-152626858	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152626130..152627645-chr1:152842015..152844012,15	MCF-7	breast:
2	chr1:152626242..152627151-chr1:152734184..152735164,3	MCF-7	breast:
3	chr1:152626393..152627202-chr1:153165098..153165609,2	MCF-7	breast:
4	chr1:152626437..152627174-chr1:152749824..152750672,3	MCF-7	breast:
5	chr1:152626165..152627303-chr1:152707558..152708767,8	MCF-7	breast:
6	chr1:152626212..152627124-chr1:152707916..152708805,6	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00302	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1011297	0.85[ASN][1000 genomes]
rs10788844	0.87[ASN][1000 genomes]
rs10888504	0.80[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10888505	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs10888506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888507	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888509	1.00[JPT][hapmap]
rs11205045	0.85[ASN][1000 genomes]
rs11205046	0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs11205047	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs11205048	0.85[ASN][1000 genomes]
rs11205049	0.85[ASN][1000 genomes]
rs11205050	0.85[ASN][1000 genomes]
rs11205056	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11205060	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11205061	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205062	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205066	0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs11205072	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205073	0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs11205078	0.86[ASN][1000 genomes]
rs11580546	0.85[ASN][1000 genomes]
rs11581621	0.85[ASN][1000 genomes]
rs11582021	0.85[ASN][1000 genomes]
rs11587218	0.85[ASN][1000 genomes]
rs12032251	0.85[ASN][1000 genomes]
rs12036739	0.82[MEX][hapmap]
rs12041270	0.85[ASN][1000 genomes]
rs12043198	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071335	0.83[ASN][1000 genomes]
rs12074783	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12081753	0.85[ASN][1000 genomes]
rs12081793	0.85[ASN][1000 genomes]
rs12239432	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239456	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12564254	0.85[ASN][1000 genomes]
rs12564476	0.83[ASN][1000 genomes]
rs12566080	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12728742	0.85[ASN][1000 genomes]
rs12745646	0.85[ASN][1000 genomes]
rs12752346	0.85[ASN][1000 genomes]
rs1325508	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1332497	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1359515	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs1359516	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474168	0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs1474169	0.85[ASN][1000 genomes]
rs1575753	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1581802	0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs1581804	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs16834343	0.82[EUR][1000 genomes]
rs1819470	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1853805	0.87[ASN][1000 genomes]
rs1886732	0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925661	0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925663	0.86[ASN][1000 genomes]
rs1930126	0.87[ASN][1000 genomes]
rs3753453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs3904414	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3904415	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3908717	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4287181	0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs4353096	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4540662	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845317	0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs4845456	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs4845457	0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs55644922	0.85[ASN][1000 genomes]
rs55687384	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59349974	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59540569	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59633986	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59863780	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60208884	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60350222	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60861680	0.85[ASN][1000 genomes]
rs66587527	0.89[ASN][1000 genomes]
rs6660162	0.85[ASN][1000 genomes]
rs6662989	0.85[ASN][1000 genomes]
rs6671975	0.85[ASN][1000 genomes]
rs6687570	0.85[ASN][1000 genomes]
rs6687682	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs6702474	0.85[ASN][1000 genomes]
rs73009167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527788	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs908929	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs925976	0.90[CHB][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs925977	0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs942826	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs942827	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs960752	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs989831	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989832	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989833	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989834	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9970033	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs9970657	0.85[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	esv2750810	chr1:152453669-152660927	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1827111	chr1:152472839-152690073	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv1830764	chr1:152472839-152690073	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv33483	chr1:152550269-152775526	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv872447	chr1:152551276-152643160	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv547891	chr1:152556085-152770446	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv872448	chr1:152561408-152643160	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv469873	chr1:152563260-152713616	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv482518	chr1:152563260-152713616	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1001647	chr1:152572876-152678509	Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv872449	chr1:152583678-152643160	Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
16	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152625200-152628200	Weak transcription	NHLF	lung
2	chr1:152626400-152626600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:152626400-152626600	Enhancers	NHEK	skin
4	chr1:152626400-152627000	Enhancers	Fetal Stomach	stomach
5	chr1:152626400-152627200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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