Variant report

Variant	rs58630066
Chromosome Location	chr4:102889514-102889515
allele	G/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	GATA3	chr4:102889029-102889784	MCF-7	breast:	n/a	chr4:102889255-102889271
2	GATA3	chr4:102889106-102889583	A549	lung:	n/a	chr4:102889255-102889271
3	SP1	chr4:102888938-102889727	A549	lung:	n/a	chr4:102889296-102889310 chr4:102889301-102889310 chr4:102889299-102889311 chr4:102889300-102889309 chr4:102889300-102889310 chr4:102889299-102889311
4	EP300	chr4:102889015-102889728	A549	lung:	n/a	chr4:102889029-102889038
5	TCF12	chr4:102888920-102889954	A549	lung:	n/a	n/a
6	NR2F2	chr4:102889058-102889683	MCF-7	breast:	n/a	n/a
7	GATA3	chr4:102888882-102889866	A549	lung:	n/a	chr4:102889808-102889818 chr4:102889255-102889271
8	TEAD4	chr4:102889141-102889641	A549	lung:	n/a	n/a
9	HDAC2	chr4:102889178-102889689	MCF-7	breast:	n/a	n/a
10	FOSL2	chr4:102889188-102889606	MCF-7	breast:	n/a	n/a
11	BCL3	chr4:102889110-102889709	A549	lung:	n/a	n/a
12	FOSL2	chr4:102888806-102889671	A549	lung:	n/a	chr4:102889029-102889037 chr4:102889028-102889038 chr4:102889028-102889038 chr4:102889028-102889038 chr4:102889029-102889037 chr4:102889027-102889039 chr4:102889028-102889038 chr4:102889029-102889036
13	GATA3	chr4:102888965-102889800	MCF-7	breast:	n/a	chr4:102889255-102889271
14	EP300	chr4:102888836-102889817	A549	lung:	n/a	chr4:102889029-102889038
15	MAFK	chr4:102889282-102889626	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr4:102889412-102889522	MCF10A-Er-Src	breast:	n/a	n/a
17	REST	chr4:102889082-102889586	A549	lung:	n/a	chr4:102889297-102889310
18	BRCA1	chr4:102889042-102889556	Hela-S3	cervix:	n/a	n/a
19	FOXA2	chr4:102889187-102889553	A549	lung:	n/a	n/a
20	SIN3AK20	chr4:102889114-102889825	MCF-7	breast:	n/a	n/a
21	SP1	chr4:102889056-102889622	A549	lung:	n/a	chr4:102889296-102889310 chr4:102889301-102889310 chr4:102889299-102889311 chr4:102889300-102889309 chr4:102889300-102889310 chr4:102889299-102889311
22	EP300	chr4:102889129-102889727	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
MTND5P5	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10516485	0.82[ASN][1000 genomes]
rs1352173	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1486573	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16996753	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17031698	0.82[ASN][1000 genomes]
rs17031705	0.82[ASN][1000 genomes]
rs17031709	0.89[ASN][1000 genomes]
rs17031752	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17031772	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17031808	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17031827	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17031842	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17031852	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17031854	1.00[AMR][1000 genomes]
rs17031862	1.00[AMR][1000 genomes]
rs17031870	1.00[AMR][1000 genomes]
rs17031876	1.00[AMR][1000 genomes]
rs1833499	0.93[ASN][1000 genomes]
rs2276333	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276334	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2866392	1.00[ASN][1000 genomes]
rs41347351	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41516147	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4356916	0.82[ASN][1000 genomes]
rs55952681	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56757011	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56803425	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57545925	1.00[AMR][1000 genomes]
rs58588907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58846155	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59656969	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59859836	1.00[AMR][1000 genomes]
rs59893832	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60180803	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61067451	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61546925	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72929967	1.00[AMR][1000 genomes]
rs72933903	1.00[AMR][1000 genomes]
rs73834511	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73834519	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73834520	1.00[AFR][1000 genomes]
rs73834525	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73834537	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73834541	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73834547	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73834549	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv999861	chr4:102576115-102930562	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2757945	chr4:102662699-103008940	Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759269	chr4:102662699-103008940	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1011180	chr4:102685236-102985945	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537202	chr4:102685236-102985945	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2757074	chr4:102772861-102933949	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879682	chr4:102859835-103088491	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102882600-102889600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:102883400-102891400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:102883600-102889800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:102883600-102891400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:102888000-102890400	Enhancers	Hela-S3	cervix
6	chr4:102888600-102890400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:102888800-102889800	Enhancers	NHDF-Ad	bronchial
8	chr4:102888800-102890000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:102888800-102890000	Enhancers	Osteobl	bone
10	chr4:102889200-102889600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:102889200-102889600	Enhancers	HMEC	breast
12	chr4:102889200-102889800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:102889200-102890400	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr4:102889200-102890600	Enhancers	Stomach Mucosa	stomach
15	chr4:102889400-102889600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:102889400-102889800	Active TSS	A549	lung
17	chr4:102889400-102891000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:102889400-102897800	Weak transcription	NH-A	brain

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