Variant report

Variant	rs116147381
Chromosome Location	chr3:20081303-20081304
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	CTCF	chr3:20081180-20081330	HCT-116	colon:	n/a	n/a
2	TAF1	chr3:20081107-20081350	GM12878	blood:	n/a	n/a
3	CTCF	chr3:20081228-20081348	Kidney_OC	kidney:	n/a	n/a
4	CTCF	chr3:20081240-20081390	GM12872	blood:	n/a	n/a
5	RAD21	chr3:20081249-20081769	A549	lung:	n/a	chr3:20081384-20081393 chr3:20081386-20081399
6	RAD21	chr3:20081190-20081651	MCF-7	breast:	n/a	chr3:20081384-20081393 chr3:20081386-20081399
7	POLR2A	chr3:20081162-20083287	GM18951	blood:	n/a	n/a
8	POLR2A	chr3:20081128-20083325	Raji	blood:	n/a	n/a
9	MAZ	chr3:20080789-20082657	GM12878	blood:	n/a	chr3:20080865-20080872 chr3:20081324-20081334 chr3:20081371-20081381
10	POLR2A	chr3:20081116-20083279	GM18526	blood:	n/a	n/a
11	CTCF	chr3:20081275-20081305	Lung_OC	lung:	n/a	n/a
12	IRF1	chr3:20080209-20081645	K562	blood:	n/a	chr3:20081139-20081153 chr3:20081139-20081149
13	CTCF	chr3:20081107-20081708	K562	blood:	n/a	chr3:20081459-20081469 chr3:20081385-20081393 chr3:20081385-20081398 chr3:20081462-20081471 chr3:20081456-20081474
14	RUNX3	chr3:20081156-20081826	GM12878	blood:	n/a	n/a
15	CTCF	chr3:20081068-20083345	K562	blood:	n/a	chr3:20081459-20081469 chr3:20082835-20082848 chr3:20082833-20082851 chr3:20081385-20081393 chr3:20081385-20081398 chr3:20081462-20081471 chr3:20081456-20081474
16	NR2F2	chr3:20080924-20081754	K562	blood:	n/a	n/a
17	MAZ	chr3:20081169-20083287	Hela-S3	cervix:	n/a	chr3:20081324-20081334 chr3:20081371-20081381 chr3:20083104-20083114
18	CTCF	chr3:20081280-20081430	WI-38	lung:	n/a	chr3:20081385-20081393 chr3:20081385-20081398
19	CTCF	chr3:20081261-20081668	GM19238	blood:	n/a	chr3:20081459-20081469 chr3:20081385-20081393 chr3:20081385-20081398 chr3:20081462-20081471 chr3:20081456-20081474
20	BCLAF1	chr3:20081249-20081751	GM12878	blood:	n/a	chr3:20081692-20081705 chr3:20081686-20081699 chr3:20081365-20081374 chr3:20081683-20081696 chr3:20081685-20081698 chr3:20081684-20081693 chr3:20081691-20081704
21	SMC3	chr3:20081300-20081670	K562	blood:	n/a	chr3:20081458-20081472 chr3:20081629-20081639
22	POLR2A	chr3:20081119-20081849	GM12878	blood:	n/a	n/a
23	MXI1	chr3:20081079-20081733	K562	blood:	n/a	n/a
24	MAZ	chr3:20080936-20083371	IMR90	lung:	n/a	chr3:20081324-20081334 chr3:20081371-20081381 chr3:20083104-20083114
25	PAX5	chr3:20081280-20081755	GM12892	blood:	n/a	n/a
26	POLR2A	chr3:20081119-20081811	GM12892	blood:	n/a	n/a
27	YY1	chr3:20081300-20082459	GM12892	blood:	n/a	chr3:20081916-20081925 chr3:20081696-20081707 chr3:20081919-20081928 chr3:20081683-20081697 chr3:20081362-20081373 chr3:20081913-20081927 chr3:20081922-20081931 chr3:20081683-20081692 chr3:20081917-20081928 chr3:20081920-20081931 chr3:20081916-20081930 chr3:20081686-20081700 chr3:20081919-20081933
28	CTCF	chr3:20081160-20081310	AG10803	skin:	n/a	n/a
29	MAX	chr3:20081219-20081808	K562	blood:	n/a	chr3:20081324-20081334 chr3:20081371-20081381
30	TBL1XR1	chr3:20081054-20081728	GM12878	blood:	n/a	n/a
31	RAD21	chr3:20081205-20081727	H1-hESC	embryonic stem cell:	n/a	chr3:20081384-20081393 chr3:20081386-20081399
32	MAX	chr3:20081237-20081807	A549	lung:	n/a	chr3:20081324-20081334 chr3:20081371-20081381
33	CTCF	chr3:20081035-20081782	MCF-7	breast:	n/a	chr3:20081459-20081469 chr3:20081385-20081393 chr3:20081385-20081398 chr3:20081462-20081471 chr3:20081456-20081474
34	BRCA1	chr3:20081212-20081617	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:20080965-20083309	GM18505	blood:	n/a	n/a
36	ZBTB7A	chr3:20081195-20081581	HepG2	liver:	n/a	chr3:20081457-20081466
37	SMC3	chr3:20081099-20081686	GM12878	blood:	n/a	chr3:20081458-20081472 chr3:20081629-20081639
38	FOXP2	chr3:20081285-20081727	PFSK-1	brain:	n/a	n/a
39	CTCF	chr3:20081119-20081838	K562	blood:	n/a	chr3:20081459-20081469 chr3:20081385-20081393 chr3:20081385-20081398 chr3:20081462-20081471 chr3:20081456-20081474
40	MAX	chr3:20081250-20083332	K562	blood:	n/a	chr3:20081324-20081334 chr3:20081371-20081381 chr3:20083104-20083114
41	MYC	chr3:20080133-20083357	K562	blood:	n/a	chr3:20080865-20080872 chr3:20081324-20081334 chr3:20081371-20081381 chr3:20083104-20083114
42	CTCF	chr3:20081290-20081618	T-47D	breast:	n/a	chr3:20081459-20081469 chr3:20081385-20081393 chr3:20081385-20081398 chr3:20081462-20081471 chr3:20081456-20081474
43	MAX	chr3:20081277-20081775	ECC-1	luminal epithelium:	n/a	chr3:20081324-20081334 chr3:20081371-20081381
44	HDAC2	chr3:20081253-20081618	K562	blood:	n/a	n/a
45	RAD21	chr3:20081240-20081717	ECC-1	luminal epithelium:	n/a	chr3:20081384-20081393 chr3:20081386-20081399
46	POLR2A	chr3:20081216-20082059	GM12878	blood:	n/a	n/a
47	SMC3	chr3:20081157-20081686	Hela-S3	cervix:	n/a	chr3:20081458-20081472 chr3:20081629-20081639
48	MAZ	chr3:20080126-20083442	K562	blood:	n/a	chr3:20080865-20080872 chr3:20081324-20081334 chr3:20081371-20081381 chr3:20083104-20083114
49	CTCFL	chr3:20081114-20081593	K562	blood:	n/a	chr3:20081458-20081467
50	RCOR1	chr3:20081062-20081727	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:20079279..20082964-chr3:20226299..20229620,6	K562	blood:
2	chr3:20079527..20082964-chr3:20226742..20229620,4	K562	blood:
3	chr3:20036427..20038510-chr3:20080865..20083451,2	K562	blood:
4	chr3:20079693..20081472-chr3:20203928..20206383,2	K562	blood:
5	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:
6	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
7	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:

Variant related genes	Relation type
KAT2B	TF binding region
ENSG00000144566	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000201545	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv3396791	chr3:20080148-20083246	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	esv3426803	chr3:20080473-20083321	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 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	chr3:20080000-20083200	Active TSS	Aorta	Aorta
2	chr3:20080200-20081400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr3:20080200-20083200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:20080200-20083200	Active TSS	Left Ventricle	heart
5	chr3:20080200-20083200	Active TSS	Ovary	ovary
6	chr3:20080200-20083200	Active TSS	NHLF	lung
7	chr3:20080200-20083400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr3:20080200-20083400	Active TSS	Colon Smooth Muscle	Colon
9	chr3:20080400-20081800	Active TSS	Right Atrium	heart
10	chr3:20080400-20082400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:20080400-20082600	Active TSS	Brain Germinal Matrix	brain
12	chr3:20080400-20082600	Active TSS	Colonic Mucosa	Colon
13	chr3:20080400-20082800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:20080400-20083200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:20080400-20083200	Active TSS	Fetal Brain Female	brain
16	chr3:20080400-20083200	Active TSS	Fetal Kidney	kidney
17	chr3:20080400-20083200	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:20080400-20083400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:20080400-20083400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:20080400-20083400	Active TSS	Psoas Muscle	Psoas
21	chr3:20080400-20083600	Active TSS	Right Ventricle	heart
22	chr3:20080400-20083800	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr3:20080600-20081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:20080600-20081400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:20080600-20081600	Active TSS	Fetal Heart	heart
26	chr3:20080600-20082200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr3:20080600-20082400	Active TSS	Fetal Muscle Trunk	muscle
28	chr3:20080600-20082600	Active TSS	Placenta	Placenta
29	chr3:20080600-20082600	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:20080600-20082600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr3:20080600-20082800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr3:20080600-20082800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr3:20080600-20082800	Active TSS	Stomach Smooth Muscle	stomach
34	chr3:20080600-20083000	Active TSS	Duodenum Mucosa	Duodenum
35	chr3:20080600-20083200	Active TSS	Brain Substantia Nigra	brain
36	chr3:20080600-20083200	Active TSS	Lung	lung
37	chr3:20080600-20083200	Active TSS	Stomach Mucosa	stomach
38	chr3:20080600-20083200	Active TSS	GM12878-XiMat	blood
39	chr3:20080600-20083200	Active TSS	NHDF-Ad	bronchial
40	chr3:20080600-20083400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:20080600-20083400	Active TSS	Thymus	Thymus
42	chr3:20080600-20083600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:20080800-20082400	Active TSS	Primary T cells fromperipheralblood	blood
44	chr3:20080800-20082400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:20080800-20082400	Active TSS	NHEK	skin
46	chr3:20080800-20082600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr3:20080800-20082600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:20080800-20082600	Active TSS	Adipose Nuclei	Adipose
49	chr3:20080800-20082600	Active TSS	Liver	Liver
50	chr3:20080800-20082600	Active TSS	Fetal Stomach	stomach

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