Variant report

Variant	rs2999557
Chromosome Location	chr1:151971707-151971708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr1:151971252-151971867	A549	lung:	n/a	n/a
2	FOS	chr1:151971144-151971868	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:151971423-151971842	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA2	chr1:151971262-151971841	A549	lung:	n/a	n/a
5	TCF12	chr1:151971088-151971999	A549	lung:	n/a	n/a
6	MYC	chr1:151971407-151971805	MCF10A-Er-Src	breast:	n/a	chr1:151971637-151971646
7	RAD21	chr1:151971540-151971716	Hela-S3	cervix:	n/a	n/a
8	EP300	chr1:151971311-151971818	Hela-S3	cervix:	n/a	chr1:151971783-151971797
9	NR2F2	chr1:151970551-151971953	MCF-7	breast:	n/a	n/a
10	ESR1	chr1:151971372-151971814	ECC-1	luminal epithelium:	n/a	n/a
11	JUND	chr1:151971332-151971842	A549	lung:	n/a	n/a
12	MYC	chr1:151971353-151971805	MCF10A-Er-Src	breast:	n/a	chr1:151971637-151971646
13	FOSL2	chr1:151971005-151971936	A549	lung:	n/a	n/a
14	EP300	chr1:151971140-151972000	A549	lung:	n/a	chr1:151971783-151971797
15	TEAD4	chr1:151971087-151971821	A549	lung:	n/a	n/a
16	NFIC	chr1:151971298-151971864	ECC-1	luminal epithelium:	n/a	n/a
17	STAT3	chr1:151971336-151971832	MCF10A-Er-Src	breast:	n/a	chr1:151971716-151971724
18	FOXA1	chr1:151971448-151971728	T-47D	breast:	n/a	n/a
19	STAT3	chr1:151971367-151971782	MCF10A-Er-Src	breast:	n/a	chr1:151971716-151971724
20	MAX	chr1:151971167-151972355	A549	lung:	n/a	chr1:151971637-151971646
21	EP300	chr1:151971039-151971947	A549	lung:	n/a	chr1:151971783-151971797
22	ESR1	chr1:151971313-151971752	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr1:151971541-151971866	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr1:151971294-151971863	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr1:151971348-151971872	ECC-1	luminal epithelium:	n/a	chr1:151971637-151971646
26	JUN	chr1:151971608-151971827	HepG2	liver:	n/a	n/a
27	SIN3AK20	chr1:151971385-151971746	A549	lung:	n/a	n/a
28	MAX	chr1:151971183-151971896	A549	lung:	n/a	chr1:151971637-151971646
29	GATA3	chr1:151971009-151972064	MCF-7	breast:	n/a	n/a
30	NR3C1	chr1:151971437-151971712	ECC-1	luminal epithelium:	n/a	n/a
31	FOSL2	chr1:151971395-151971862	A549	lung:	n/a	n/a
32	TCF12	chr1:151971128-151971922	ECC-1	luminal epithelium:	n/a	n/a
33	STAT3	chr1:151971500-151971733	MCF10A-Er-Src	breast:	n/a	chr1:151971716-151971724
34	NR2F2	chr1:151971132-151971952	MCF-7	breast:	n/a	n/a
35	FOSL2	chr1:151971522-151971734	HepG2	liver:	n/a	n/a
36	CEBPB	chr1:151971579-151971727	HepG2	liver:	n/a	n/a
37	ESR1	chr1:151971382-151971771	ECC-1	luminal epithelium:	n/a	n/a
38	CEBPB	chr1:151971387-151971972	A549	lung:	n/a	chr1:151971529-151971546
39	SMC3	chr1:151971299-151971809	Hela-S3	cervix:	n/a	n/a
40	FOXA2	chr1:151971396-151971883	A549	lung:	n/a	n/a
41	RFX5	chr1:151971570-151971764	Hela-S3	cervix:	n/a	n/a
42	ATF3	chr1:151971247-151971791	A549	lung:	n/a	n/a
43	NR3C1	chr1:151971440-151971843	A549	lung:	n/a	n/a
44	SP1	chr1:151971127-151971894	A549	lung:	n/a	n/a
45	TEAD4	chr1:151970912-151971866	ECC-1	luminal epithelium:	n/a	n/a
46	GATA3	chr1:151971410-151971840	T-47D	breast:	n/a	n/a
47	FOXA1	chr1:151971473-151971728	ECC-1	luminal epithelium:	n/a	n/a
48	SP1	chr1:151971140-151971889	A549	lung:	n/a	n/a
49	GATA3	chr1:151970979-151971934	MCF-7	breast:	n/a	n/a
50	NR3C1	chr1:151971376-151971765	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:
2	chr1:151940563..151941140-chr1:151971510..151972483,2	MCF-7	breast:
3	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
4	chr1:151905903..151909731-chr1:151970506..151972835,3	MCF-7	breast:
5	chr1:151969792..151972069-chr1:152018129..152020747,2	K562	blood:
6	chr1:151803574..151806321-chr1:151969156..151972059,2	MCF-7	breast:
7	chr1:151859844..151863422-chr1:151970039..151972808,5	MCF-7	breast:
8	chr1:151823821..151827198-chr1:151970881..151974396,3	MCF-7	breast:

No data

Variant related genes	Relation type
S100A10	TF binding region
ENSG00000143365	Chromatin interaction
ENSG00000196407	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10788811	1.00[AMR][1000 genomes]
rs2338205	1.00[AMR][1000 genomes]
rs2999521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2999549	1.00[AMR][1000 genomes]
rs3007675	1.00[AMR][1000 genomes]
rs3007683	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007715	1.00[AMR][1000 genomes]
rs3104206	1.00[AMR][1000 genomes]
rs7551161	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong 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 target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151966800-151976800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151967000-151973000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:151967000-151977000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:151967200-151973200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:151967200-151974000	Enhancers	HMEC	breast
6	chr1:151967200-151977000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:151967800-151973600	Enhancers	NHEK	skin
8	chr1:151967800-151973800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:151967800-151977200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:151968000-151973000	Weak transcription	Adipose Nuclei	Adipose
11	chr1:151968200-151973000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:151968200-151973200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:151968200-151973400	Weak transcription	HepG2	liver
14	chr1:151968200-151973400	Weak transcription	Osteobl	bone
15	chr1:151968200-151973600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:151968400-151972800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:151968600-151973600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:151968600-151973600	Weak transcription	HSMM	muscle
19	chr1:151968800-151973800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:151969400-151971800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:151969400-151973800	Weak transcription	Placenta	Placenta
22	chr1:151970200-151972000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:151970200-151972600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:151970200-151973000	Weak transcription	NHDF-Ad	bronchial
25	chr1:151970600-151972800	Enhancers	Hela-S3	cervix
26	chr1:151970800-151972000	Weak transcription	Esophagus	oesophagus
27	chr1:151970800-151972400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:151971000-151972000	Enhancers	Stomach Mucosa	stomach
29	chr1:151971000-151972400	Enhancers	Fetal Intestine Large	intestine
30	chr1:151971000-151974400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:151971200-151971800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:151971200-151972000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr1:151971400-151971800	Enhancers	NH-A	brain
34	chr1:151971400-151972200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:151971400-151972200	Enhancers	Fetal Intestine Small	intestine
36	chr1:151971600-151971800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:151971600-151972400	Enhancers	H9 Cell Line	embryonic stem cell
38	chr1:151971600-151972400	Flanking Active TSS	A549	lung

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