Variant report

Variant	rs548255638
Chromosome Location	chr1:57110389-57110390
allele	C/T
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	E2F6	chr1:57110344-57111389	H1-hESC	embryonic stem cell:	n/a	chr1:57111003-57111013 chr1:57111006-57111016 chr1:57111000-57111010
2	MAX	chr1:57110265-57111822	A549	lung:	n/a	n/a
3	SIN3A	chr1:57110362-57110713	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr1:57110073-57112051	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr1:57109756-57111909	IMR90	lung:	n/a	n/a
6	POLR2A	chr1:57110217-57111688	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:57110266-57111698	HEK293	kidney:	n/a	n/a
8	RFX5	chr1:57109929-57110739	Hela-S3	cervix:	n/a	n/a
9	ZNF263	chr1:57110045-57110764	HEK293-T-REx	kidney:	n/a	n/a
10	POLR2A	chr1:57110270-57111232	Hela-S3	cervix:	n/a	n/a
11	SMARCB1	chr1:57109860-57111913	Hela-S3	cervix:	n/a	n/a
12	MAX	chr1:57110365-57111746	HepG2	liver:	n/a	n/a
13	CHD2	chr1:57110314-57111134	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr1:57110340-57110899	A549	lung:	n/a	n/a
15	POLR2A	chr1:57110339-57111757	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr1:57110267-57111969	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:57110068-57112007	Hela-S3	cervix:	n/a	n/a
18	TBP	chr1:57109814-57110582	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr1:57109959-57110542	Hela-S3	cervix:	n/a	n/a
20	ZBTB7A	chr1:57110267-57111426	ECC-1	luminal epithelium:	n/a	n/a
21	BRCA1	chr1:57109886-57110415	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:57110276-57111893	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:57109759-57112147	Hela-S3	cervix:	n/a	n/a
24	REST	chr1:57110268-57112005	H1-neurons	neurons:	n/a	chr1:57110757-57110767 chr1:57110821-57110831 chr1:57110714-57110732 chr1:57110975-57110988 chr1:57110779-57110797 chr1:57111028-57111041 chr1:57111263-57111276
25	TAF1	chr1:57110287-57110554	Hela-S3	cervix:	n/a	n/a
26	MAZ	chr1:57110319-57111885	Hela-S3	cervix:	n/a	n/a
27	MAX	chr1:57110040-57111965	Hela-S3	cervix:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf168-2	chr1:57109889-57110681	XLOC_000846

Variant related genes	Relation type
PRKAA2	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3371942	chr1:57109389-57112237	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3402388	chr1:57109989-57112537	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3445991	chr1:57110114-57112162	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57109800-57110400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:57109800-57110400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr1:57109800-57110600	Flanking Active TSS	HUVEC	blood vessel
4	chr1:57109800-57110800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:57109800-57111000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:57109800-57111200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:57109800-57111400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
8	chr1:57109800-57111600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:57109800-57111600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:57109800-57111800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr1:57109800-57112000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:57109800-57112000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:57109800-57112000	Active TSS	Psoas Muscle	Psoas
14	chr1:57109800-57112200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:57109800-57112200	Active TSS	Brain Angular Gyrus	brain
16	chr1:57109800-57112400	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:57109800-57113200	Active TSS	Right Atrium	heart
18	chr1:57109800-57114600	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:57110000-57110400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
20	chr1:57110000-57110400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr1:57110000-57110400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:57110000-57110400	Enhancers	Brain Substantia Nigra	brain
23	chr1:57110000-57110400	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr1:57110000-57110400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr1:57110000-57110400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
26	chr1:57110000-57110400	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr1:57110000-57110400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:57110000-57110600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:57110000-57110600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr1:57110000-57110600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:57110000-57110800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:57110000-57110800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:57110000-57110800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:57110000-57110800	Flanking Active TSS	Liver	Liver
35	chr1:57110000-57110800	Bivalent/Poised TSS	Stomach Mucosa	stomach
36	chr1:57110000-57111400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:57110000-57111400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:57110000-57111400	Active TSS	NH-A	brain
39	chr1:57110000-57111600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:57110000-57111600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
41	chr1:57110000-57111600	Active TSS	Fetal Lung	lung
42	chr1:57110000-57111600	Active TSS	Ovary	ovary
43	chr1:57110000-57111800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr1:57110000-57112000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr1:57110000-57112000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:57110000-57112000	Active TSS	Fetal Brain Female	brain
47	chr1:57110000-57112000	Bivalent/Poised TSS	Osteobl	bone
48	chr1:57110000-57112200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:57110000-57112200	Active TSS	Brain Cingulate Gyrus	brain
50	chr1:57110000-57112200	Active TSS	Hela-S3	cervix

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