Variant report

Variant	rs535099815
Chromosome Location	chr3:120067961-120067962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:512)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:512 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr3:120067680-120068108	GM12878	blood:	n/a	n/a
2	BACH1	chr3:120067855-120068693	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr3:120067749-120068678	K562	blood:	n/a	chr3:120068105-120068114
4	FOSL2	chr3:120067802-120068825	A549	lung:	n/a	n/a
5	ZNF384	chr3:120067854-120068628	K562	blood:	n/a	n/a
6	HDAC2	chr3:120067471-120068157	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:120067813-120068055	MCF-7	breast:	n/a	n/a
8	TAL1	chr3:120067878-120068441	K562	blood:	n/a	n/a
9	MAX	chr3:120067739-120068656	H1-hESC	embryonic stem cell:	n/a	chr3:120068105-120068114
10	E2F4	chr3:120067351-120068779	K562	blood:	n/a	n/a
11	CTCF	chr3:120067920-120068070	NB4	blood:	n/a	n/a
12	ELK4	chr3:120067923-120068523	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:120067709-120068876	U87	brain:	n/a	n/a
14	POLR2A	chr3:120067426-120068676	GM12892	blood:	n/a	n/a
15	MYC	chr3:120066869-120068791	NB4	blood:	n/a	chr3:120068105-120068114
16	CTCF	chr3:120067759-120068307	MCF-7	breast:	n/a	n/a
17	MYC	chr3:120067840-120068432	HepG2	liver:	n/a	chr3:120068105-120068114
18	SP1	chr3:120067659-120068586	A549	lung:	n/a	chr3:120068277-120068286
19	CTCF	chr3:120067675-120068296	IMR90	lung:	n/a	n/a
20	E2F6	chr3:120067321-120068602	K562	blood:	n/a	n/a
21	POLR2A	chr3:120067843-120068886	SK-N-MC	brain:	n/a	n/a
22	USF1	chr3:120067774-120068913	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:120067742-120068542	GM12891	blood:	n/a	n/a
24	MYC	chr3:120067601-120068889	K562	blood:	n/a	chr3:120068105-120068114
25	FOXA2	chr3:120067791-120068614	A549	lung:	n/a	n/a
26	CTCF	chr3:120067812-120068069	GM19239	blood:	n/a	n/a
27	CTCF	chr3:120067860-120068010	GM06990	blood:	n/a	n/a
28	POLR2A	chr3:120067606-120068685	HUVEC	blood vessel:	n/a	n/a
29	MAX	chr3:120066805-120068834	MCF-7	breast:	n/a	chr3:120068105-120068114
30	POLR2A	chr3:120067447-120068601	A549	lung:	n/a	n/a
31	USF1	chr3:120067525-120068855	HCT-116	colon:	n/a	n/a
32	POLR2A	chr3:120067804-120068763	PANC-1	pancreas:	n/a	n/a
33	ELF1	chr3:120067811-120068736	GM12878	blood:	n/a	chr3:120068278-120068290
34	TEAD4	chr3:120067839-120068499	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr3:120067512-120068576	MCF-7	breast:	n/a	chr3:120068105-120068114
36	POLR2A	chr3:120067809-120068600	SK-N-SH	brain:	n/a	n/a
37	REST	chr3:120067685-120067967	ECC-1	luminal epithelium:	n/a	n/a
38	HMGN3	chr3:120067498-120068570	K562	blood:	n/a	n/a
39	POLR2A	chr3:120067517-120068645	PANC-1	pancreas:	n/a	n/a
40	CEBPB	chr3:120067870-120068476	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr3:120067372-120068677	GM12892	blood:	n/a	n/a
42	GABPA	chr3:120067762-120068566	A549	lung:	n/a	chr3:120068131-120068140
43	REST	chr3:120067757-120068506	A549	lung:	n/a	n/a
44	PML	chr3:120067125-120068824	GM12878	blood:	n/a	chr3:120067478-120067486
45	MAX	chr3:120067668-120068857	SK-N-SH	brain:	n/a	chr3:120068105-120068114
46	MXI1	chr3:120066827-120068840	IMR90	lung:	n/a	n/a
47	POLR2A	chr3:120067563-120068568	GM12891	blood:	n/a	n/a
48	MXI1	chr3:120067632-120067998	H1-hESC	embryonic stem cell:	n/a	n/a
49	JUND	chr3:120067628-120068594	A549	lung:	n/a	n/a
50	E2F4	chr3:120067570-120068793	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:119962878..119965844-chr3:120065668..120069448,4	MCF-7	breast:
2	chr11:65382893..65383727-chr3:120067505..120068255,2	Hela-S3	cervix:
3	chr3:120066931..120069030-chr3:120314504..120317461,2	MCF-7	breast:
4	chr19:47615199..47615964-chr3:120067825..120068376,2	NB4	blood:
5	chr3:120055756..120058586-chr3:120065980..120068170,2	K562	blood:
6	chr3:119961553..119963645-chr3:120067756..120069896,2	MCF-7	breast:
7	chr3:119813314..119815193-chr3:120066557..120069483,2	MCF-7	breast:
8	chr3:120066981..120069399-chr3:120202784..120204698,2	MCF-7	breast:
9	chr3:120066130..120068617-chr3:120117930..120119437,2	K562	blood:
10	chr3:113464641..113465236-chr3:120067876..120068653,2	NB4	blood:
11	chr3:119811895..119815177-chr3:120067061..120069801,4	K562	blood:
12	chr10:104503487..104504043-chr3:120067799..120068315,2	Hela-S3	cervix:
13	chr3:120066467..120068992-chr3:120105411..120108399,2	MCF-7	breast:
14	chr3:120002820..120005702-chr3:120066388..120068289,2	MCF-7	breast:
15	chr3:119814026..119816300-chr3:120067212..120070079,2	MCF-7	breast:
16	chr3:119810967..119815661-chr3:120066752..120069801,5	K562	blood:
17	chr3:120067385..120069387-chr3:120120673..120122492,2	MCF-7	breast:
18	chr2:233414846..233415548-chr3:120067893..120068661,3	HCT-116	colon:

No data

Variant related genes	Relation type
ENSG00000240661	TF binding region
ENSG00000166272	Chromatin interaction
ENSG00000242613	Chromatin interaction
ENSG00000130749	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000135930	Chromatin interaction
ENSG00000240774	Chromatin interaction
ENSG00000175697	Chromatin interaction
ENSG00000266620	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000242622	Chromatin interaction
ENSG00000121579	Chromatin interaction
ENSG00000065518	Chromatin interaction
ENSG00000221944	Chromatin interaction
ENSG00000163430	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv236293	chr3:120066250-120069861	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
12	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv3968	chr3:120066454-120111463	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120066600-120069000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:120066600-120069000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:120066600-120069000	Active TSS	Right Atrium	heart
4	chr3:120066600-120069200	Active TSS	NHLF	lung
5	chr3:120066600-120069400	Active TSS	Ovary	ovary
6	chr3:120066800-120068000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr3:120066800-120068600	Active TSS	Colonic Mucosa	Colon
8	chr3:120066800-120068800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:120066800-120068800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr3:120066800-120068800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:120066800-120069000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:120066800-120069000	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:120066800-120069000	Active TSS	Psoas Muscle	Psoas
14	chr3:120066800-120069000	Active TSS	Right Ventricle	heart
15	chr3:120066800-120069000	Active TSS	A549	lung
16	chr3:120066800-120069200	Active TSS	Brain Substantia Nigra	brain
17	chr3:120066800-120069200	Active TSS	GM12878-XiMat	blood
18	chr3:120066800-120069400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:120066800-120069400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:120067000-120068800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:120067000-120069000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:120067000-120069200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:120067000-120069400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:120067000-120069400	Active TSS	HSMM	muscle
25	chr3:120067000-120069400	Active TSS	NHDF-Ad	bronchial
26	chr3:120067000-120069600	Active TSS	HMEC	breast
27	chr3:120067200-120068400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr3:120067200-120068400	Active TSS	Dnd41	blood
29	chr3:120067200-120068600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:120067200-120068600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr3:120067200-120068600	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr3:120067200-120068600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:120067200-120068600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:120067200-120068600	Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:120067200-120068600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr3:120067200-120068800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:120067200-120068800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:120067200-120068800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:120067200-120068800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:120067200-120068800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:120067200-120068800	Active TSS	Brain Cingulate Gyrus	brain
42	chr3:120067200-120068800	Active TSS	Esophagus	oesophagus
43	chr3:120067200-120068800	Active TSS	Fetal Intestine Small	intestine
44	chr3:120067200-120068800	Active TSS	Gastric	stomach
45	chr3:120067200-120068800	Active TSS	Pancreas	Pancrea
46	chr3:120067200-120068800	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr3:120067200-120068800	Active TSS	Small Intestine	intestine
48	chr3:120067200-120069000	Active TSS	Fetal Intestine Large	intestine
49	chr3:120067200-120069000	Active TSS	Fetal Stomach	stomach
50	chr3:120067200-120069000	Active TSS	Left Ventricle	heart

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