Variant report

Variant	rs1923942
Chromosome Location	chr1:59246626-59246627
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:0)
Chromatin interactive
region (count:76)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:1)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:59244106-59251818	U87	brain:	n/a	n/a
2	POLR2A	chr1:59245147-59251676	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:59245334-59246889	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:59243934-59251872	U87	brain:	n/a	n/a
5	CHD1	chr1:59244118-59252745	IMR90	lung:	n/a	chr1:59250203-59250213
6	POLR2A	chr1:59246459-59247027	GM12878	blood:	n/a	n/a
7	HEY1	chr1:59246437-59251188	K562	blood:	n/a	chr1:59250260-59250275 chr1:59249195-59249210
8	POLR2A	chr1:59244614-59251725	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:59244517-59246995	HUVEC	blood vessel:	n/a	n/a
10	MAFK	chr1:59246573-59246853	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:59244523-59251294	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:59245241-59249887	K562	blood:	n/a	n/a
13	POLR2A	chr1:59246568-59246836	HCT-116	colon:	n/a	n/a
14	SMC3	chr1:59246541-59246936	HepG2	liver:	n/a	n/a
15	RCOR1	chr1:59245085-59247110	HepG2	liver:	n/a	n/a
16	CHD2	chr1:59244672-59246973	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:59246598-59246794	GM12878	blood:	n/a	n/a
18	CCNT2	chr1:59246625-59246750	K562	blood:	n/a	n/a
19	POLR2A	chr1:59244682-59251438	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:59246523-59246765	MCF-7	breast:	n/a	n/a
21	POLR2A	chr1:59245389-59246950	Hela-S3	cervix:	n/a	n/a
22	CEBPZ	chr1:59246251-59246861	HepG2	liver:	n/a	n/a
23	MAX	chr1:59245600-59251175	HepG2	liver:	n/a	chr1:59249843-59249852
24	POLR2A	chr1:59245312-59247006	GM12892	blood:	n/a	n/a
25	TCF7L2	chr1:59245460-59246715	HEK293	kidney:	n/a	chr1:59245652-59245661
26	POLR2A	chr1:59243686-59251714	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr1:59246594-59246860	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr1:59246497-59246641	ProgFib	skin:	n/a	n/a
29	POLR2A	chr1:59245391-59247001	GM12892	blood:	n/a	n/a
30	REST	chr1:59246413-59251517	H1-neurons	neurons:	n/a	chr1:59249842-59249851 chr1:59249082-59249100 chr1:59249081-59249101 chr1:59251217-59251231
31	POLR2A	chr1:59246453-59246946	GM12891	blood:	n/a	n/a
32	POLR2A	chr1:59244543-59251831	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr1:59243934-59251878	U87	brain:	n/a	n/a
34	POLR2A	chr1:59245266-59246983	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:59246515-59246895	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:59246111-59247022	Hela-S3	cervix:	n/a	n/a
37	JUND	chr1:59244731-59247038	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr1:59244510-59251644	K562	blood:	n/a	n/a
39	KAP1	chr1:59245324-59246879	HEK293	kidney:	n/a	n/a
40	ARID3A	chr1:59244726-59247751	HepG2	liver:	n/a	n/a
41	NFYB	chr1:59246265-59246684	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:59245215-59246882	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr1:59244754-59251746	PANC-1	pancreas:	n/a	n/a
44	MAZ	chr1:59244647-59251811	IMR90	lung:	n/a	chr1:59249843-59249852
45	POLR2A	chr1:59244499-59247115	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:59244292-59251292	HUVEC	blood vessel:	n/a	n/a
47	CHD2	chr1:59245338-59247907	K562	blood:	n/a	n/a
48	POLR2A	chr1:59246180-59246871	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:59244100-59250835	A549	lung:	n/a	n/a
50	POLR2A	chr1:59246551-59251299	H1-neurons	neurons:	n/a	n/a

No data

(count:76 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr1:59244361..59246823-chr1:59649097..59651993,2	K562	blood:
2	chr1:59244855..59247331-chr1:59314391..59317376,3	K562	blood:
3	chr1:59245914..59247946-chr1:59568208..59571099,2	K562	blood:
4	chr1:59244768..59246699-chr1:59759656..59762805,3	K562	blood:
5	chr1:59208975..59211483-chr1:59245941..59247562,2	MCF-7	breast:
6	chr1:59245185..59249625-chr1:59318506..59322949,5	K562	blood:
7	chr1:59245650..59249709-chr1:60164316..60166597,3	MCF-7	breast:
8	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
9	chr1:59245313..59247577-chr1:59481237..59483014,2	K562	blood:
10	chr1:59244693..59246755-chr1:60196068..60197895,2	K562	blood:
11	chr1:28973695..28976366-chr1:59244298..59247179,2	K562	blood:
12	chr1:59246163..59248652-chr1:59466870..59469148,2	K562	blood:
13	chr1:59246529..59249235-chr1:59474703..59476422,2	K562	blood:
14	chr1:59245578..59252912-chr1:59759683..59766457,13	MCF-7	breast:
15	chr1:59246264..59248102-chr1:149855755..149857816,2	MCF-7	breast:
16	chr1:59244238..59248031-chr1:59689062..59692608,4	K562	blood:
17	chr1:59245157..59247090-chr1:59636264..59638828,2	K562	blood:
18	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
19	chr1:59245589..59247526-chr1:59439230..59441535,3	K562	blood:
20	chr1:59245136..59249509-chr1:59544104..59550391,6	K562	blood:
21	chr1:59246525..59249398-chr1:60121634..60124612,2	K562	blood:
22	chr1:59245974..59248964-chr1:60182800..60185774,2	MCF-7	breast:
23	chr1:59244169..59247698-chr1:60062396..60065400,3	K562	blood:
24	chr1:59244855..59247592-chr1:59314391..59317376,4	K562	blood:
25	chr1:59244079..59247030-chr1:60125320..60128311,2	K562	blood:
26	chr1:59244923..59247251-chr1:59843655..59845229,2	K562	blood:
27	chr1:59192672..59194770-chr1:59244784..59246788,2	MCF-7	breast:
28	chr1:59186058..59188120-chr1:59245328..59247867,2	K562	blood:
29	chr1:59245887..59249534-chr1:59455949..59458682,3	K562	blood:
30	chr1:59244053..59249750-chr1:59393075..59399809,12	K562	blood:
31	chr1:59246435..59249254-chr1:59487144..59489692,2	MCF-7	breast:
32	chr1:59244169..59247928-chr1:60060481..60064138,5	K562	blood:
33	chr1:59244161..59247403-chr1:59832378..59835096,3	K562	blood:
34	chr1:59203533..59207535-chr1:59246122..59248670,4	K562	blood:
35	chr1:59245573..59247756-chr1:59431368..59433217,2	K562	blood:
36	chr1:59208278..59211622-chr1:59243472..59246717,6	K562	blood:
37	chr1:59246122..59248225-chr1:60208395..60212049,3	K562	blood:
38	chr1:59245164..59246849-chr1:59463690..59466367,2	K562	blood:
39	chr1:59245718..59248161-chr1:59323277..59324885,2	MCF-7	breast:
40	chr1:59191433..59194290-chr1:59244978..59247044,2	K562	blood:
41	chr1:59163564..59170812-chr1:59245390..59251956,13	K562	blood:
42	chr1:59245604..59247254-chr1:59311635..59313742,2	K562	blood:
43	chr1:59245933..59248490-chr1:59559542..59562151,2	K562	blood:
44	chr1:59245570..59248484-chr1:61782798..61784305,2	K562	blood:
45	chr1:59244876..59251429-chr1:59540803..59548111,10	K562	blood:
46	chr1:59244785..59246783-chr1:59553913..59556142,2	K562	blood:
47	chr1:59245275..59248106-chr1:59562308..59564391,2	K562	blood:
48	chr1:59244236..59247273-chr1:59648638..59651433,3	K562	blood:
49	chr1:59245909..59247878-chr1:59481525..59484880,3	K562	blood:
50	chr1:59244465..59246813-chr1:60227285..60230046,2	K562	blood:

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	JUN	hsa-miR-29c-3p	chr1:59246616-59246639

Variant related genes	Relation type
LINC01135	TF binding region
ENSG00000231740	Chromatin interaction
ENSG00000235215	Chromatin interaction
ENSG00000272226	Chromatin interaction
ENSG00000162601	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000264081	Chromatin interaction
ENSG00000232453	Chromatin interaction
ENSG00000228121	Chromatin interaction
ENSG00000172456	Chromatin interaction
ENSG00000222168	Chromatin interaction
JUN	miRNA target site

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2179658	1.00[AMR][1000 genomes]
rs4647008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	esv1798968	chr1:59246581-59251097	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1799803	chr1:59246581-59251097	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59239800-59247200	Weak transcription	Esophagus	oesophagus
2	chr1:59239800-59247400	Weak transcription	Gastric	stomach
3	chr1:59243200-59247200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:59245200-59247000	Enhancers	Hela-S3	cervix
5	chr1:59245200-59251400	Active TSS	Aorta	Aorta
6	chr1:59245400-59247000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr1:59245400-59247600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:59245600-59246800	Flanking Active TSS	NHEK	skin
9	chr1:59245600-59247000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:59245600-59247000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:59245600-59247200	Flanking Active TSS	Fetal Lung	lung
12	chr1:59245600-59247400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:59245600-59247400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:59245600-59247600	Active TSS	Right Ventricle	heart
15	chr1:59245600-59247600	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:59245600-59250600	Active TSS	HMEC	breast
17	chr1:59245600-59251000	Active TSS	HSMMtube	muscle
18	chr1:59245600-59251400	Active TSS	Psoas Muscle	Psoas
19	chr1:59245800-59246800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:59245800-59246800	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:59245800-59247000	Flanking Active TSS	Fetal Heart	heart
22	chr1:59245800-59247200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:59245800-59247200	Active TSS	Fetal Intestine Small	intestine
24	chr1:59245800-59247200	Enhancers	HepG2	liver
25	chr1:59245800-59248400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:59245800-59248400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
27	chr1:59245800-59248800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
28	chr1:59246000-59246800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:59246000-59247000	Active TSS	Adipose Nuclei	Adipose
30	chr1:59246000-59247200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:59246000-59247200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:59246000-59247400	Active TSS	NHLF	lung
33	chr1:59246000-59247600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:59246000-59247800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:59246000-59248000	Active TSS	Right Atrium	heart
36	chr1:59246000-59248400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:59246000-59251200	Active TSS	Liver	Liver
38	chr1:59246200-59247000	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:59246200-59247000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:59246200-59247400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:59246200-59247400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
42	chr1:59246200-59247600	Flanking Active TSS	Fetal Brain Male	brain
43	chr1:59246200-59248800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:59246200-59251600	Active TSS	Fetal Kidney	kidney
45	chr1:59246400-59246800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:59246400-59246800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:59246400-59246800	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr1:59246400-59247000	Enhancers	Primary B cells from cord blood	blood
49	chr1:59246400-59247000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr1:59246400-59247000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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