Variant report

Variant	rs553824056
Chromosome Location	chr3:23959044-23959045
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:417)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:417 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:23958138-23959197	A549	lung:	n/a	n/a
2	EP300	chr3:23958064-23959381	A549	lung:	n/a	n/a
3	RUNX3	chr3:23957822-23959408	GM12878	blood:	n/a	n/a
4	ATF2	chr3:23958232-23959402	H1-hESC	embryonic stem cell:	n/a	n/a
5	ETS1	chr3:23957956-23959417	K562	blood:	n/a	chr3:23958534-23958547 chr3:23958533-23958546 chr3:23958596-23958607
6	RELA	chr3:23958138-23959259	GM15510	blood:	n/a	n/a
7	HEY1	chr3:23958136-23959699	HepG2	liver:	n/a	chr3:23958483-23958498
8	POLR2A	chr3:23958105-23960665	K562	blood:	n/a	n/a
9	YY1	chr3:23958063-23959381	K562	blood:	n/a	chr3:23958483-23958494 chr3:23958485-23958494 chr3:23958491-23958505
10	POLR2A	chr3:23957987-23959405	K562	blood:	n/a	n/a
11	ELK1	chr3:23958050-23959249	K562	blood:	n/a	n/a
12	GTF2F1	chr3:23958020-23959283	Hela-S3	cervix:	n/a	n/a
13	YY1	chr3:23958448-23959331	GM12892	blood:	n/a	chr3:23958483-23958494 chr3:23958485-23958494 chr3:23958491-23958505
14	SIX5	chr3:23958037-23959387	A549	lung:	n/a	chr3:23958533-23958547 chr3:23958537-23958546 chr3:23958535-23958544
15	JUND	chr3:23958469-23959248	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:23958098-23960725	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:23958121-23960749	SK-N-SH	brain:	n/a	n/a
18	ELF1	chr3:23958899-23959283	SK-N-SH	brain:	n/a	n/a
19	EP300	chr3:23958302-23959238	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:23958042-23960224	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:23958118-23960215	GM12891	blood:	n/a	n/a
22	TAF1	chr3:23958269-23959240	GM12878	blood:	n/a	n/a
23	CREB1	chr3:23957957-23959395	HepG2	liver:	n/a	n/a
24	GABPA	chr3:23958016-23959458	MCF-7	breast:	n/a	n/a
25	POLR2A	chr3:23957960-23959774	GM12878	blood:	n/a	n/a
26	CEBPB	chr3:23958317-23959420	K562	blood:	n/a	n/a
27	POLR2A	chr3:23958170-23960433	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr3:23958032-23960247	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:23958128-23960836	K562	blood:	n/a	n/a
30	CHD1	chr3:23957214-23960192	IMR90	lung:	n/a	n/a
31	POLR2A	chr3:23957643-23960742	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:23957917-23960298	Hela-S3	cervix:	n/a	n/a
33	GABPA	chr3:23958206-23959355	SK-N-SH	brain:	n/a	n/a
34	MYC	chr3:23957965-23959701	K562	blood:	n/a	n/a
35	POLR2A	chr3:23958070-23960273	HepG2	liver:	n/a	n/a
36	MAX	chr3:23957973-23959300	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:23957917-23960748	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:23958045-23963842	GM12878	blood:	n/a	n/a
39	TEAD4	chr3:23958312-23959306	A549	lung:	n/a	n/a
40	POLR2A	chr3:23958067-23959351	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:23959007-23959229	HepG2	liver:	n/a	n/a
42	RELA	chr3:23957828-23959253	GM18951	blood:	n/a	n/a
43	PAX5	chr3:23957996-23959242	GM12892	blood:	n/a	n/a
44	REST	chr3:23958158-23959419	HL-60	blood:	n/a	chr3:23958595-23958608 chr3:23958203-23958212
45	RCOR1	chr3:23958069-23959062	HepG2	liver:	n/a	n/a
46	MAX	chr3:23957925-23959393	SK-N-SH	brain:	n/a	n/a
47	E2F4	chr3:23958022-23959378	K562	blood:	n/a	chr3:23958468-23958480
48	TBP	chr3:23958093-23959287	HepG2	liver:	n/a	n/a
49	SIN3A	chr3:23957682-23959805	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:23958006-23962277	GM12878	blood:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:76425682..76426603-chr3:23958326..23959064,2	HCT-116	colon:
2	chr3:23846380..23850116-chr3:23956700..23960461,6	MCF-7	breast:
3	chr17:7387027..7387912-chr3:23958534..23959086,2	HCT-116	colon:
4	chr3:23958569..23960911-chr3:24534140..24537048,3	MCF-7	breast:
5	chr3:23850301..23853237-chr3:23957517..23960615,4	MCF-7	breast:
6	chr3:23958135..23959121-chrX:47003925..47004575,2	NB4	blood:
7	chr15:42787482..42788209-chr3:23958299..23959137,2	Hela-S3	cervix:
8	chr11:62358928..62359477-chr3:23958548..23959210,2	Hela-S3	cervix:
9	chr17:58167241..58170093-chr3:23957521..23960210,2	MCF-7	breast:
10	chr12:49524707..49525421-chr3:23958490..23959051,2	Hela-S3	cervix:
11	chr3:23957476..23960072-chr3:25467685..25470119,2	K562	blood:
12	chr3:23958447..23959124-chr7:139025718..139026246,2	Hela-S3	cervix:
13	chr3:23958536..23961065-chr3:24535525..24538143,3	K562	blood:
14	chr3:23956080..23959048-chr3:23995915..23997492,2	MCF-7	breast:
15	chr3:23845393..23848355-chr3:23958587..23960710,4	K562	blood:
16	chr1:203059673..203062550-chr3:23957552..23960185,2	MCF-7	breast:
17	chr3:23852479..23855481-chr3:23956917..23960502,4	MCF-7	breast:
18	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
19	chr3:12873721..12876260-chr3:23958650..23961334,2	K562	blood:
20	chr16:1661843..1662391-chr3:23958190..23959085,2	Hela-S3	cervix:
21	chr3:23957534..23959919-chr3:25823926..25825755,2	K562	blood:
22	chr3:23848988..23853074-chr3:23957156..23960234,5	K562	blood:
23	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
24	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
25	chr3:23957572..23960051-chr3:23995970..23999234,5	MCF-7	breast:

No data

Variant related genes	Relation type
RPL15	TF binding region
NKIRAS1	TF binding region
ENSG00000147123	Chromatin interaction
ENSG00000163485	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000077092	Chromatin interaction
ENSG00000151093	Chromatin interaction
ENSG00000272263	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000151092	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000187535	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000261040	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000164898	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000007545	Chromatin interaction
ENSG00000182872	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23956800-23959200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:23956800-23959400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:23956800-23959400	Active TSS	Brain Angular Gyrus	brain
4	chr3:23957000-23959400	Active TSS	Colon Smooth Muscle	Colon
5	chr3:23957000-23959600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:23957000-23959600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:23957000-23959600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:23957000-23960400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:23957000-23960600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:23957000-23960600	Active TSS	Right Atrium	heart
11	chr3:23957200-23959400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:23957200-23959600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:23957200-23959600	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:23957200-23959600	Active TSS	HSMMtube	muscle
15	chr3:23957200-23960200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:23957200-23960800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:23957400-23959200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:23957400-23959400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:23957400-23959400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:23957400-23959400	Active TSS	HSMM	muscle
21	chr3:23957400-23959600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:23957400-23959600	Active TSS	Brain Anterior Caudate	brain
23	chr3:23957400-23959600	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:23957400-23959600	Active TSS	Fetal Stomach	stomach
25	chr3:23957400-23959600	Active TSS	Left Ventricle	heart
26	chr3:23957400-23959600	Active TSS	Rectal Smooth Muscle	rectum
27	chr3:23957400-23959600	Active TSS	GM12878-XiMat	blood
28	chr3:23957400-23959600	Active TSS	NHDF-Ad	bronchial
29	chr3:23957400-23959800	Active TSS	Ovary	ovary
30	chr3:23957400-23960800	Active TSS	Psoas Muscle	Psoas
31	chr3:23957400-23960800	Active TSS	Right Ventricle	heart
32	chr3:23957600-23959200	Active TSS	NHEK	skin
33	chr3:23957600-23959400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:23957600-23959400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:23957600-23959400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:23957600-23959400	Active TSS	Brain Substantia Nigra	brain
37	chr3:23957600-23959400	Active TSS	Fetal Brain Female	brain
38	chr3:23957600-23959400	Active TSS	Fetal Lung	lung
39	chr3:23957600-23959400	Active TSS	NHLF	lung
40	chr3:23957600-23959600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:23957600-23959600	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr3:23957600-23959600	Active TSS	Liver	Liver
43	chr3:23957600-23959600	Active TSS	Brain Hippocampus Middle	brain
44	chr3:23957600-23959600	Active TSS	Fetal Brain Male	brain
45	chr3:23957600-23959600	Active TSS	Fetal Intestine Large	intestine
46	chr3:23957600-23959600	Active TSS	Fetal Muscle Trunk	muscle
47	chr3:23957600-23959600	Active TSS	Placenta	Placenta
48	chr3:23957600-23959600	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:23957600-23959600	Bivalent/Poised TSS	HepG2	liver
50	chr3:23957600-23960200	Active TSS	Fetal Intestine Small	intestine

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