Variant report

Variant	rs9839834
Chromosome Location	chr3:139073138-139073139
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	CTCF	chr3:139072694-139073237	T-47D	breast:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
2	CTCF	chr3:139073020-139073170	A549	lung:	n/a	n/a
3	POLR2A	chr3:139072709-139073185	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr3:139069653-139075359	GM12878	blood:	n/a	n/a
5	CTCF	chr3:139072689-139073205	HepG2	liver:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
6	ARID3A	chr3:139072609-139073255	K562	blood:	n/a	n/a
7	STAT3	chr3:139072581-139073380	MCF10A-Er-Src	breast:	n/a	n/a
8	ZNF143	chr3:139072817-139073143	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:139072746-139073253	A549	lung:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
10	CTCF	chr3:139072718-139073383	K562	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
11	RAD21	chr3:139072775-139073239	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:139070258-139074075	U87	brain:	n/a	n/a
13	CTCF	chr3:139072697-139073237	K562	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
14	USF2	chr3:139072811-139073174	Hela-S3	cervix:	n/a	n/a
15	ZC3H11A	chr3:139072865-139073472	K562	blood:	n/a	n/a
16	POLR2A	chr3:139069657-139075279	GM12891	blood:	n/a	n/a
17	MAZ	chr3:139072794-139073140	K562	blood:	n/a	n/a
18	CTCF	chr3:139072620-139073304	MCF-7	breast:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
19	POLR2A	chr3:139072709-139073334	SK-N-SH	brain:	n/a	n/a
20	EP300	chr3:139072740-139073149	K562	blood:	n/a	n/a
21	CTCF	chr3:139072382-139073439	SK-N-SH	brain:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
22	SMC3	chr3:139072813-139073181	K562	blood:	n/a	n/a
23	POLR2A	chr3:139070257-139075369	GM12878	blood:	n/a	n/a
24	RAD21	chr3:139072802-139073176	SK-N-SH_RA	brain:	n/a	n/a
25	CTCF	chr3:139072725-139073235	MCF-7	breast:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
26	POLR2A	chr3:139069579-139081379	K562	blood:	n/a	n/a
27	CTCF	chr3:139072662-139073197	IMR90	lung:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
28	POLR2A	chr3:139072192-139075180	Hela-S3	cervix:	n/a	n/a
29	PML	chr3:139072770-139073155	K562	blood:	n/a	n/a
30	RAD21	chr3:139072639-139073307	HCT-116	colon:	n/a	n/a
31	POLR2A	chr3:139073110-139073368	MCF-7	breast:	n/a	n/a
32	TBL1XR1	chr3:139072734-139073387	K562	blood:	n/a	n/a
33	ZNF143	chr3:139072802-139073185	K562	blood:	n/a	n/a
34	POLR2A	chr3:139072773-139073766	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr3:139072794-139073161	A549	lung:	n/a	n/a
36	CTCF	chr3:139072632-139073357	HCT-116	colon:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
37	RAD21	chr3:139072779-139073167	Hela-S3	cervix:	n/a	n/a
38	ZMIZ1	chr3:139072881-139073241	K562	blood:	n/a	n/a
39	POLR2A	chr3:139072750-139074216	HepG2	liver:	n/a	n/a
40	RAD21	chr3:139072809-139073237	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr3:139072228-139077148	K562	blood:	n/a	n/a
42	POLR2A	chr3:139072747-139075259	K562	blood:	n/a	n/a
43	POLR2A	chr3:139072854-139075604	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:139072784-139073807	PANC-1	pancreas:	n/a	n/a
45	CTCF	chr3:139072779-139073164	A549	lung:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
46	RUNX3	chr3:139072772-139073143	GM12878	blood:	n/a	chr3:139072972-139072987
47	E2F4	chr3:139072722-139073187	MCF10A-Er-Src	breast:	n/a	n/a
48	CTCF	chr3:139072624-139073305	K562	blood:	n/a	chr3:139072991-139073007 chr3:139072990-139073008
49	POLR2A	chr3:139072930-139075138	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:139072381-139075342	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139072256..139074431-chr3:139078607..139080931,2	MCF-7	breast:
2	chr3:139072544..139073416-chr3:139280346..139281512,5	MCF-7	breast:
3	chr3:139047930..139048680-chr3:139072548..139073494,2	K562	blood:
4	chr3:139073016..139076494-chr3:139077200..139080091,3	MCF-7	breast:
5	chr3:139072091..139074896-chr3:139076494..139078712,3	K562	blood:
6	chr3:138847869..138848524-chr3:139072496..139073303,2	K562	blood:
7	chr3:138830352..138831184-chr3:139072519..139073327,2	MCF-7	breast:
8	chr3:139072193..139074257-chr3:139106179..139110026,3	MCF-7	breast:
9	chr3:139072517..139075084-chr3:139096841..139099787,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272656	TF binding region
ENSG00000184432	Chromatin interaction
ENSG00000248932	Chromatin interaction
ENSG00000252245	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12695695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13325144	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28545366	1.00[AFR][1000 genomes]
rs34654084	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35586329	1.00[AFR][1000 genomes]
rs71314515	0.83[AFR][1000 genomes]
rs9820144	1.00[AFR][1000 genomes]
rs9846449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9874641	0.83[AMR][1000 genomes]
rs9878661	0.82[EUR][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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription 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	10 gene(s)	inside rSNPs	diseases
3	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
6	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
7	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
8	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
9	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
10	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:139065000-139103800	Strong transcription	HSMM	muscle
12	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:139065200-139073200	Strong transcription	K562	blood
15	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:139065400-139073800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:139065400-139102600	Strong transcription	Osteobl	bone
29	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
31	chr3:139065600-139073200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:139065600-139077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:139065600-139079600	Strong transcription	Fetal Lung	lung
34	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
40	chr3:139065600-139103600	Strong transcription	NH-A	brain
41	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:139065800-139074200	Strong transcription	Adipose Nuclei	Adipose
44	chr3:139065800-139078000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:139065800-139080800	Strong transcription	Brain Germinal Matrix	brain
46	chr3:139065800-139081000	Strong transcription	Fetal Brain Female	brain
47	chr3:139065800-139095000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:139065800-139096200	Strong transcription	Liver	Liver
49	chr3:139065800-139098200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:139065800-139098200	Strong transcription	HMEC	breast

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