Variant report

Variant	rs557884107
Chromosome Location	chr3:48699198-48699199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:247)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:247 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr3:48699111-48699446	GM12891	blood:	n/a	n/a
2	YY1	chr3:48699061-48699405	K562	blood:	n/a	n/a
3	ELF1	chr3:48699094-48699370	K562	blood:	n/a	n/a
4	REST	chr3:48698992-48699711	PFSK-1	brain:	n/a	n/a
5	SIN3AK20	chr3:48698909-48699720	MCF-7	breast:	n/a	n/a
6	CHD1	chr3:48698915-48699304	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr3:48699044-48699520	MCF-7	breast:	n/a	n/a
8	SIN3A	chr3:48698800-48699957	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr3:48699127-48699502	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr3:48699068-48699500	HepG2	liver:	n/a	n/a
11	RFX5	chr3:48699140-48699384	K562	blood:	n/a	n/a
12	HDAC2	chr3:48699083-48699475	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:48699003-48699419	HUVEC	blood vessel:	n/a	n/a
14	NFIC	chr3:48699110-48699434	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr3:48699102-48699488	A549	lung:	n/a	n/a
16	POLR2A	chr3:48698961-48699783	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr3:48698829-48700050	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:48699179-48699355	Spleen_OC	spleen:	n/a	n/a
19	SPI1	chr3:48699094-48699372	GM12878	blood:	n/a	n/a
20	ZBTB7A	chr3:48698860-48699499	ECC-1	luminal epithelium:	n/a	n/a
21	RUNX3	chr3:48699076-48699436	GM12878	blood:	n/a	n/a
22	ELF1	chr3:48698877-48699851	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:48698903-48702611	H1-hESC	embryonic stem cell:	n/a	n/a
24	REST	chr3:48698726-48700055	PFSK-1	brain:	n/a	n/a
25	MAZ	chr3:48699183-48699482	HepG2	liver:	n/a	n/a
26	SREBP1	chr3:48698687-48699855	GM12878	blood:	n/a	n/a
27	ATF2	chr3:48699005-48699484	H1-hESC	embryonic stem cell:	n/a	n/a
28	STAT1	chr3:48699131-48699376	GM12878	blood:	n/a	n/a
29	ETS1	chr3:48699021-48699500	K562	blood:	n/a	n/a
30	REST	chr3:48698585-48700084	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr3:48698971-48699691	MCF-7	breast:	n/a	n/a
32	NRF1	chr3:48699127-48699374	HepG2	liver:	n/a	chr3:48699249-48699260
33	ATF2	chr3:48699029-48699495	GM12878	blood:	n/a	n/a
34	TAF7	chr3:48699015-48699538	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYBL2	chr3:48698930-48699549	HepG2	liver:	n/a	n/a
36	RCOR1	chr3:48699089-48699629	GM12878	blood:	n/a	n/a
37	MAX	chr3:48699099-48699396	K562	blood:	n/a	n/a
38	SIN3AK20	chr3:48699062-48699437	PANC-1	pancreas:	n/a	n/a
39	ZMIZ1	chr3:48699154-48699375	K562	blood:	n/a	n/a
40	HDAC2	chr3:48699059-48699424	MCF-7	breast:	n/a	n/a
41	PAX5	chr3:48698846-48699413	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr3:48699068-48699464	H1-hESC	embryonic stem cell:	n/a	n/a
43	CHD2	chr3:48699103-48699431	K562	blood:	n/a	n/a
44	REST	chr3:48698881-48699818	PANC-1	pancreas:	n/a	n/a
45	REST	chr3:48698779-48699894	H1-hESC	embryonic stem cell:	n/a	n/a
46	ARID3A	chr3:48699155-48699487	HepG2	liver:	n/a	n/a
47	NR2F2	chr3:48698995-48699502	K562	blood:	n/a	n/a
48	SIN3AK20	chr3:48698880-48699604	H1-hESC	embryonic stem cell:	n/a	n/a
49	POU2F2	chr3:48699139-48699509	GM12878	blood:	n/a	n/a
50	YY1	chr3:48699049-48699487	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:48697809..48699544-chr3:49049957..49052349,2	MCF-7	breast:
2	chr3:48670997..48674874-chr3:48698947..48702118,7	MCF-7	breast:
3	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
4	chr3:48695950..48699824-chr3:48710158..48713070,3	K562	blood:
5	chr3:48698351..48700757-chr3:49057854..49060697,2	K562	blood:
6	chr3:48670764..48674544-chr3:48699167..48702803,6	K562	blood:
7	chr3:48698197..48700148-chr3:48700175..48701734,2	MCF-7	breast:
8	chr3:48675163..48677992-chr3:48697938..48699928,2	K562	blood:
9	chr3:48670764..48674544-chr3:48698929..48702803,9	K562	blood:
10	chr3:48647141..48648853-chr3:48697785..48700969,3	MCF-7	breast:
11	chr3:48698738..48703197-chr3:48713751..48717809,8	K562	blood:
12	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
13	chr3:48659070..48661619-chr3:48697247..48699239,2	K562	blood:
14	chr3:48678686..48683466-chr3:48696483..48700259,5	K562	blood:
15	chr3:48686566..48688475-chr3:48697453..48700260,2	MCF-7	breast:
16	chr3:48593030..48597118-chr3:48698507..48702121,6	MCF-7	breast:
17	chr3:48602276..48604378-chr3:48697664..48699278,2	K562	blood:
18	chr3:48678987..48680520-chr3:48698680..48701564,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228350	TF binding region
ENSG00000178252	Chromatin interaction
ENSG00000183396	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000207605	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	esv3359935	chr3:48696498-48699296	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
10	esv3409347	chr3:48697698-48701896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv822075	chr3:48698492-48699585	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48697800-48699800	Weak transcription	A549	lung
2	chr3:48698400-48699400	Enhancers	Ovary	ovary
3	chr3:48698400-48700000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:48698400-48700400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:48698400-48700400	Enhancers	Fetal Heart	heart
6	chr3:48698400-48700600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr3:48698400-48700800	Enhancers	Lung	lung
8	chr3:48698400-48701800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:48698600-48699200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:48698600-48699200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:48698600-48699200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:48698600-48699400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:48698600-48699400	Flanking Active TSS	Pancreas	Pancrea
14	chr3:48698600-48699400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
15	chr3:48698600-48699600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
16	chr3:48698600-48699600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr3:48698600-48699600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:48698600-48699600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
19	chr3:48698600-48699800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:48698600-48700000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
21	chr3:48698600-48700000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr3:48698600-48700000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:48698600-48700200	Enhancers	Gastric	stomach
24	chr3:48698600-48700200	Enhancers	HMEC	breast
25	chr3:48698600-48700400	Active TSS	Brain Cingulate Gyrus	brain
26	chr3:48698600-48701800	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:48698600-48702400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr3:48698800-48699200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:48698800-48699200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:48698800-48699200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:48698800-48699200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:48698800-48699200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
34	chr3:48698800-48699200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
36	chr3:48698800-48699200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:48698800-48699200	Flanking Active TSS	Fetal Brain Female	brain
39	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Placenta	Placenta
42	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
43	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
44	chr3:48698800-48699200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
45	chr3:48698800-48699200	Bivalent Enhancer	Psoas Muscle	Psoas
46	chr3:48698800-48699200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
47	chr3:48698800-48699200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr3:48698800-48699200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr3:48698800-48699200	Bivalent Enhancer	Small Intestine	intestine
50	chr3:48698800-48699200	Flanking Active TSS	Osteobl	bone

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