Variant report

Variant	rs4688059
Chromosome Location	chr3:119811568-119811569
allele	A/G
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	chr3:119811468-119811687	SH-SY5Y	brain:	n/a	chr3:119811497-119811518
2	MAX	chr3:119811344-119815256	Hela-S3	cervix:	n/a	chr3:119812593-119812612
3	STAT3	chr3:119811524-119811632	MCF10A-Er-Src	breast:	n/a	n/a
4	RFX5	chr3:119810327-119815428	SK-N-SH	brain:	n/a	chr3:119815376-119815385 chr3:119814006-119814015 chr3:119813079-119813094 chr3:119813666-119813674 chr3:119813487-119813496 chr3:119813036-119813052 chr3:119813676-119813685 chr3:119813933-119813942
5	RFX5	chr3:119811246-119815261	Hela-S3	cervix:	n/a	chr3:119814006-119814015 chr3:119813079-119813094 chr3:119813666-119813674 chr3:119813487-119813496 chr3:119813036-119813052 chr3:119813676-119813685 chr3:119813933-119813942
6	ZNF263	chr3:119811548-119814992	HEK293-T-REx	kidney:	n/a	n/a
7	TBP	chr3:119811298-119811847	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119810967..119815661-chr3:120066752..120069801,5	K562	blood:
2	chr3:119710167..119712500-chr3:119810883..119812424,2	MCF-7	breast:
3	chr3:119717186..119719857-chr3:119810036..119812260,3	K562	blood:
4	chr3:119594389..119596043-chr3:119808975..119811664,2	K562	blood:

Variant related genes	Relation type
ENSG00000242622	TF binding region
ENSG00000240661	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10934503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12054090	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12108149	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12629015	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12630592	0.81[JPT][hapmap]
rs12630829	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632325	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12634476	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12634889	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12635018	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12638973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13321783	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1574154	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17204878	0.81[JPT][hapmap]
rs1870931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980718	0.83[ASN][1000 genomes]
rs2319398	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2319399	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs28536662	0.81[JPT][hapmap]
rs28831519	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs334533	0.81[JPT][hapmap]
rs334563	0.81[JPT][hapmap]
rs4340737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4688042	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4688046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688053	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688054	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58863896	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60235167	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264714	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62264734	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62264739	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264747	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264749	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62266274	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62266277	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62266281	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438552	0.81[JPT][hapmap]
rs6792572	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs6797459	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7431209	0.81[JPT][hapmap]
rs7639388	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7644234	0.81[JPT][hapmap]
rs9873477	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9878473	0.81[JPT][hapmap]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:119804600-119812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:119804600-119812000	Weak transcription	Pancreas	Pancrea
4	chr3:119805600-119812000	Weak transcription	Gastric	stomach
5	chr3:119808000-119814800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:119808000-119816400	Active TSS	Fetal Brain Female	brain
7	chr3:119808200-119814800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:119808200-119815000	Active TSS	HMEC	breast
9	chr3:119808400-119812800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:119808400-119815600	Active TSS	GM12878-XiMat	blood
11	chr3:119808600-119814800	Active TSS	NHEK	skin
12	chr3:119808800-119815000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:119808800-119815600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:119809000-119811800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:119809000-119812800	Active TSS	Right Atrium	heart
16	chr3:119809000-119815000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:119809000-119816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:119809200-119812000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr3:119809200-119812200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:119809200-119812600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr3:119809200-119814800	Active TSS	Brain Angular Gyrus	brain
22	chr3:119809200-119814800	Active TSS	NH-A	brain
23	chr3:119809200-119815000	Active TSS	HSMMtube	muscle
24	chr3:119809200-119815400	Active TSS	Psoas Muscle	Psoas
25	chr3:119809200-119815400	Active TSS	Right Ventricle	heart
26	chr3:119809200-119815600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:119809200-119815600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:119809200-119815800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:119809200-119816000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:119809200-119816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:119809400-119812000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:119809400-119812200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr3:119809400-119812600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr3:119809400-119814800	Active TSS	Stomach Smooth Muscle	stomach
35	chr3:119809400-119815000	Active TSS	Fetal Thymus	thymus
36	chr3:119809400-119815000	Active TSS	Ovary	ovary
37	chr3:119809400-119815200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:119809400-119815400	Active TSS	Aorta	Aorta
39	chr3:119809400-119815600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:119809400-119815800	Active TSS	HSMM	muscle
41	chr3:119809400-119816000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr3:119809600-119812600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr3:119809600-119812800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr3:119809600-119814800	Active TSS	Colonic Mucosa	Colon
45	chr3:119809600-119814800	Active TSS	Fetal Kidney	kidney
46	chr3:119809600-119814800	Active TSS	Fetal Stomach	stomach
47	chr3:119809600-119815000	Active TSS	Fetal Intestine Large	intestine
48	chr3:119809600-119815000	Active TSS	Fetal Lung	lung
49	chr3:119809600-119815000	Active TSS	Fetal Muscle Leg	muscle
50	chr3:119809600-119815200	Active TSS	Left Ventricle	heart

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