Variant report

Variant	rs548399525
Chromosome Location	chr3:23960604-23960605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:23960562-23961017	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:23958105-23960665	K562	blood:	n/a	n/a
3	CHD1	chr3:23960208-23960648	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:23958098-23960725	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:23960037-23960639	U87	brain:	n/a	n/a
6	POLR2A	chr3:23958121-23960749	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:23959915-23960781	HCT-116	colon:	n/a	n/a
8	POLR2A	chr3:23958128-23960836	K562	blood:	n/a	n/a
9	POLR2A	chr3:23957643-23960742	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:23957917-23960748	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:23958045-23963842	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:23958006-23962277	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:23959981-23960646	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr3:23960381-23960702	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:23957976-23965870	K562	blood:	n/a	n/a
16	POLR2A	chr3:23958037-23960741	U87	brain:	n/a	n/a
17	POLR2A	chr3:23957870-23963941	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:23958125-23960796	K562	blood:	n/a	n/a
19	POLR2A	chr3:23958144-23960750	A549	lung:	n/a	n/a
20	POLR2A	chr3:23958063-23960804	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:23960446-23964170	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:23960601-23961078	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:23960417-23961072	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:23957985-23960654	GM18505	blood:	n/a	n/a
25	POLR2A	chr3:23958082-23960833	K562	blood:	n/a	n/a
26	POLR2A	chr3:23959965-23960738	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr3:23958113-23964020	GM12892	blood:	n/a	n/a
28	POLR2A	chr3:23958008-23960767	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:23960359-23960627	GM12891	blood:	n/a	n/a
30	HEY1	chr3:23960360-23960736	HepG2	liver:	n/a	n/a
31	HEY1	chr3:23960475-23960977	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:23958192-23960766	K562	blood:	n/a	n/a
33	POLR2A	chr3:23957083-23960668	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr3:23960453-23960612	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr3:23958125-23960777	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:23960429-23961061	GM12892	blood:	n/a	n/a
37	CTCF	chr3:23960557-23960758	T-47D	breast:	n/a	n/a
38	POLR2A	chr3:23960328-23960652	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr3:23960491-23963226	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:23958169-23960768	HepG2	liver:	n/a	n/a
41	HEY1	chr3:23960507-23961061	K562	blood:	n/a	n/a
42	POLR2A	chr3:23958013-23960827	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr3:23960599-23964082	GM12892	blood:	n/a	n/a
44	POLR2A	chr3:23960427-23960633	K562	blood:	n/a	n/a
45	POLR2A	chr3:23957988-23964598	GM12892	blood:	n/a	n/a
46	SP1	chr3:23960600-23961182	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:23957980-23960747	U87	brain:	n/a	n/a
48	POLR2A	chr3:23960254-23960723	MCF-7	breast:	n/a	n/a
49	POLR2A	chr3:23959891-23960638	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr3:23958033-23960760	HUVEC	blood vessel:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23960526..23962863-chr3:24013920..24016141,2	K562	blood:
2	chr3:23051768..23053551-chr3:23960276..23962039,2	K562	blood:
3	chr3:23958569..23960911-chr3:24534140..24537048,3	MCF-7	breast:
4	chr3:23850301..23853237-chr3:23957517..23960615,4	MCF-7	breast:
5	chr3:23742842..23745448-chr3:23959508..23961357,2	K562	blood:
6	chr3:23748425..23751412-chr3:23960441..23962908,2	K562	blood:
7	chr3:23905396..23907030-chr3:23960105..23962888,2	K562	blood:
8	chr3:23958536..23961065-chr3:24535525..24538143,3	K562	blood:
9	chr3:23845393..23848355-chr3:23958587..23960710,4	K562	blood:
10	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
11	chr3:12873721..12876260-chr3:23958650..23961334,2	K562	blood:
12	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
13	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
14	chr3:23960325..23963916-chr3:24723703..24727555,4	MCF-7	breast:

No data

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000174738	Chromatin interaction
ENSG00000272263	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv966996	chr3:23958991-23961257	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1067849	chr3:23960157-23962549	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23957200-23960800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:23957400-23960800	Active TSS	Psoas Muscle	Psoas
3	chr3:23957400-23960800	Active TSS	Right Ventricle	heart
4	chr3:23957600-23960800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:23958400-23961200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:23958800-23960800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr3:23958800-23960800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr3:23958800-23960800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
9	chr3:23958800-23962000	Transcr. at gene 5' and 3'	A549	lung
10	chr3:23959000-23962000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:23959200-23960800	Transcr. at gene 5' and 3'	Osteobl	bone
12	chr3:23959200-23961200	Transcr. at gene 5' and 3'	NHEK	skin
13	chr3:23959200-23961400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
14	chr3:23959200-23961800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:23959200-23961800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
16	chr3:23959200-23961800	Transcr. at gene 5' and 3'	K562	blood
17	chr3:23959200-23962000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
18	chr3:23959400-23960800	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:23959400-23960800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr3:23959400-23960800	Transcr. at gene 5' and 3'	HMEC	breast
21	chr3:23959400-23960800	Transcr. at gene 5' and 3'	HSMM	muscle
22	chr3:23959400-23961200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:23959400-23961800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
24	chr3:23959400-23962000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:23959600-23960800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:23959600-23960800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:23959600-23960800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:23959600-23960800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:23959600-23960800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:23959600-23960800	Transcr. at gene 5' and 3'	Hela-S3	cervix
31	chr3:23959600-23960800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
32	chr3:23959600-23960800	Transcr. at gene 5' and 3'	NH-A	brain
33	chr3:23959600-23960800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
34	chr3:23959600-23961600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:23959600-23962000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:23959600-23962200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:23959600-23962200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
38	chr3:23959600-23965200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:23959600-23965600	Weak transcription	Spleen	Spleen
40	chr3:23959600-23969400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:23959800-23960800	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:23959800-23961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:23959800-23965000	Weak transcription	Ovary	ovary
44	chr3:23960000-23961000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:23960000-23961000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:23960000-23961600	Weak transcription	Aorta	Aorta
47	chr3:23960000-23962000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr3:23960000-23965000	Weak transcription	Colonic Mucosa	Colon
49	chr3:23960200-23960800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:23960200-23960800	Strong transcription	Fetal Muscle Trunk	muscle

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