Variant report

Variant	rs28495024
Chromosome Location	chr7:99016683-99016684
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99015966-99018331	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr7:99014266-99018235	K562	blood:	n/a	n/a
3	POLR2A	chr7:99015891-99018344	K562	blood:	n/a	n/a
4	POLR2A	chr7:99014945-99018503	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:99016385-99016853	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:99016478-99017223	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr7:99014932-99018261	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr7:99016177-99018400	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:99015057-99018434	K562	blood:	n/a	n/a
10	POLR2A	chr7:99013704-99019437	HepG2	liver:	n/a	n/a
11	POLR2A	chr7:99016465-99018216	HL-60	blood:	n/a	n/a
12	POLR2A	chr7:99016480-99016726	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:99015973-99017458	K562	blood:	n/a	n/a
14	POLR2A	chr7:99016636-99018209	A549	lung:	n/a	n/a
15	POLR2A	chr7:99015914-99018221	HepG2	liver:	n/a	n/a
16	POLR2A	chr7:99016419-99018454	GM12891	blood:	n/a	n/a
17	POLR2A	chr7:99015947-99018298	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:99015722-99017100	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr7:99015842-99016702	K562	blood:	n/a	n/a
20	POLR2A	chr7:99016003-99016997	K562	blood:	n/a	n/a
21	POLR2A	chr7:99016569-99017168	GM12892	blood:	n/a	n/a
22	POLR2A	chr7:99014958-99018400	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr7:99016336-99016982	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr7:99015741-99018451	GM12892	blood:	n/a	n/a
25	POLR2A	chr7:99015682-99018611	GM12892	blood:	n/a	n/a
26	POLR2A	chr7:99016351-99017201	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr7:99015780-99018254	K562	blood:	n/a	n/a
28	PML	chr7:99016513-99017389	K562	blood:	n/a	n/a
29	POLR2A	chr7:99016597-99018340	GM12878	blood:	n/a	n/a
30	POLR2A	chr7:99016509-99018413	GM12891	blood:	n/a	n/a
31	POLR2A	chr7:99016515-99018323	MCF-7	breast:	n/a	n/a
32	POLR2A	chr7:99015792-99018232	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr7:99015805-99018325	K562	blood:	n/a	n/a
34	POLR2A	chr7:99015853-99018459	GM12891	blood:	n/a	n/a
35	POLR2A	chr7:99016485-99016761	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:99014953-99019055	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:99014547-99019035	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99015297..99018039-chr7:99026570..99029303,2	K562	blood:
2	chr7:99014925..99017023-chr7:99029378..99031176,2	K562	blood:
3	chr7:99014760..99017430-chr7:99030939..99032749,2	MCF-7	breast:
4	chr7:99015257..99017974-chr7:99036140..99038779,2	K562	blood:
5	chr7:99014517..99016789-chr7:99055086..99057589,2	K562	blood:
6	chr7:99014835..99016757-chr7:99036121..99038779,2	K562	blood:
7	chr7:99006000..99008581-chr7:99015908..99017846,2	MCF-7	breast:
8	chr7:99015338..99018021-chr7:99021014..99023356,3	MCF-7	breast:
9	chr7:99015616..99019079-chr7:99036189..99039194,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000239133	TF binding region
ENSG00000160917	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10155966	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10236149	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10243678	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10244158	0.81[AMR][1000 genomes]
rs10249167	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10255399	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10258757	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10267346	0.83[AMR][1000 genomes]
rs10270459	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10270917	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10271049	0.81[AMR][1000 genomes]
rs10272998	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10274407	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10279308	0.85[EUR][1000 genomes]
rs1043466	0.81[AMR][1000 genomes]
rs10953287	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11762273	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11973460	0.82[AMR][1000 genomes]
rs11978089	0.85[EUR][1000 genomes]
rs13227795	0.81[AMR][1000 genomes]
rs13240600	0.80[AMR][1000 genomes]
rs1980307	0.81[AMR][1000 genomes]
rs1985453	0.86[ASN][1000 genomes]
rs2003499	0.86[EUR][1000 genomes]
rs2072181	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107922	0.87[EUR][1000 genomes]
rs2240384	0.81[AMR][1000 genomes]
rs2269985	0.84[ASN][1000 genomes]
rs2280600	0.81[AMR][1000 genomes]
rs2280601	0.81[AMR][1000 genomes]
rs2286162	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2404323	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404324	0.95[AFR][1000 genomes]
rs28457808	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28820905	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3764815	0.85[ASN][1000 genomes]
rs3801288	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59986060	0.85[ASN][1000 genomes]
rs6943920	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6953476	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6955490	0.81[EUR][1000 genomes]
rs6962772	0.81[AMR][1000 genomes]
rs6972337	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6975099	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7794682	0.81[AMR][1000 genomes]
rs883403	0.81[AMR][1000 genomes]
rs917154	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9641253	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9768020	0.83[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99007800-99024000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:99008000-99018400	Strong transcription	Gastric	stomach
4	chr7:99008000-99018400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr7:99008000-99019800	Weak transcription	Right Atrium	heart
6	chr7:99008000-99023400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:99008000-99023600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:99008000-99023800	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr7:99008000-99023800	Strong transcription	Placenta	Placenta
10	chr7:99008000-99024000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:99008000-99024000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:99008000-99024000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:99008000-99024000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:99008000-99024000	Strong transcription	Spleen	Spleen
15	chr7:99008000-99024200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr7:99008000-99024200	Strong transcription	Fetal Stomach	stomach
17	chr7:99008000-99026600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:99008200-99023400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:99008200-99023600	Strong transcription	Fetal Intestine Large	intestine
20	chr7:99008200-99023800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:99008200-99023800	Strong transcription	Fetal Brain Female	brain
22	chr7:99008200-99023800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr7:99008200-99023800	Strong transcription	Fetal Muscle Leg	muscle
24	chr7:99008200-99024000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:99008200-99024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:99008200-99024000	Strong transcription	Lung	lung
27	chr7:99008200-99024200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:99008400-99016800	Strong transcription	Thymus	Thymus
29	chr7:99008400-99018800	Strong transcription	Fetal Lung	lung
30	chr7:99008400-99018800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr7:99008400-99019000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:99008400-99019000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:99008400-99019000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr7:99008400-99019200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:99008400-99019400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:99008400-99023200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:99008400-99023400	Strong transcription	Fetal Thymus	thymus
38	chr7:99008400-99023600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:99008400-99023600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:99008400-99023600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:99008400-99023600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:99008400-99023800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:99008400-99023800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:99008400-99024000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:99008600-99017000	Weak transcription	Fetal Heart	heart
46	chr7:99008600-99018200	Strong transcription	Brain Substantia Nigra	brain
47	chr7:99008600-99018400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:99008600-99018600	Strong transcription	HMEC	breast
49	chr7:99008600-99018800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr7:99008600-99019000	Strong transcription	Primary B cells from peripheral blood	blood

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