Variant report

Variant	rs59249086
Chromosome Location	chr3:49061664-49061665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49061277-49067224	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49061230-49067176	Raji	blood:	n/a	n/a
3	POLR2A	chr3:49061378-49062333	K562	blood:	n/a	n/a
4	POLR2A	chr3:49057228-49067285	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:49057168-49067352	K562	blood:	n/a	n/a
6	POLR2A	chr3:49056705-49067193	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49061276-49064656	K562	blood:	n/a	n/a
8	POLR2A	chr3:49057429-49067153	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:49061345-49065439	K562	blood:	n/a	n/a
10	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49060280-49067138	K562	blood:	n/a	n/a
12	USF2	chr3:49061411-49061681	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:49057874-49067350	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr3:49061240-49067174	K562	blood:	n/a	n/a
15	POLR2A	chr3:49061291-49067243	HL-60	blood:	n/a	n/a
16	POLR2A	chr3:49061117-49061729	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:49056596-49067347	GM12892	blood:	n/a	n/a
18	POLR2A	chr3:49057727-49061768	ECC-1	luminal epithelium:	n/a	n/a
19	HEY1	chr3:49061235-49063812	K562	blood:	n/a	n/a
20	POLR2A	chr3:49059839-49067238	U87	brain:	n/a	n/a
21	HEY1	chr3:49061324-49064066	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:49061462-49063956	NB4	blood:	n/a	n/a
23	POLR2A	chr3:49061242-49061672	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:49061075-49067400	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr3:49061295-49064631	K562	blood:	n/a	n/a
26	POLR2A	chr3:49059865-49067325	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr3:49061444-49062343	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:49060152-49067239	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr3:49061352-49067178	K562	blood:	n/a	n/a
30	POLR2A	chr3:49061117-49067223	U87	brain:	n/a	n/a
31	POLR2A	chr3:49061408-49067223	A549	lung:	n/a	n/a
32	POLR2A	chr3:49061287-49067276	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:49061286-49064572	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:49061365-49061746	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:49057108-49067245	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:49061177-49067268	GM12891	blood:	n/a	n/a
37	POLR2A	chr3:49061227-49067304	HL-60	blood:	n/a	n/a
38	POLR2A	chr3:49061116-49067257	HCT-116	colon:	n/a	n/a
39	POLR2A	chr3:49061099-49067363	U87	brain:	n/a	n/a
40	POLR2A	chr3:49061307-49067250	GM12891	blood:	n/a	n/a
41	POLR2A	chr3:49061441-49061677	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:49061235-49067182	HEK293	kidney:	n/a	n/a
43	POLR2A	chr3:49061594-49067530	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:49061485-49067192	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:49061158-49067354	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr3:49061307-49065201	HCT-116	colon:	n/a	n/a
47	POLR2A	chr3:49060038-49067212	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr3:49061248-49067220	GM12891	blood:	n/a	n/a
49	POLR2A	chr3:49057498-49067244	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr3:49061282-49067196	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49060434..49063324-chr3:49152454..49155328,2	MCF-7	breast:
2	chr3:48964532..48967407-chr3:49057327..49061980,4	K562	blood:
3	chr3:49058992..49061753-chr3:49202909..49205077,2	MCF-7	breast:
4	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
5	chr3:49056273..49062188-chr3:49155312..49159947,7	K562	blood:
6	chr3:49060546..49063358-chr3:49081176..49082953,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR191	TF binding region
MIR425	TF binding region
DALRD3	TF binding region
ENSG00000172046	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs28533514	1.00[AMR][1000 genomes]
rs59913304	1.00[AMR][1000 genomes]
rs72931123	1.00[AMR][1000 genomes]
rs72932016	0.81[AFR][1000 genomes]
rs72932027	1.00[AMR][1000 genomes]
rs72934780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936885	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938804	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 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	chr3:49060200-49066200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:49060400-49063600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49060600-49062200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:49060600-49062600	Genic enhancers	Liver	Liver
5	chr3:49060600-49062800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:49060600-49062800	Weak transcription	Right Atrium	heart
7	chr3:49060600-49063400	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr3:49060600-49064200	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr3:49060600-49064400	Genic enhancers	Pancreas	Pancrea
10	chr3:49060600-49064800	Strong transcription	Brain Substantia Nigra	brain
11	chr3:49060600-49065200	Weak transcription	Small Intestine	intestine
12	chr3:49060600-49065600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:49060600-49065600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:49060800-49061800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:49060800-49061800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:49060800-49062000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:49060800-49062000	Strong transcription	Adipose Nuclei	Adipose
18	chr3:49060800-49062200	Genic enhancers	Fetal Intestine Large	intestine
19	chr3:49060800-49062200	Transcr. at gene 5' and 3'	Hela-S3	cervix
20	chr3:49060800-49062600	Strong transcription	Lung	lung
21	chr3:49060800-49062600	Strong transcription	HSMM	muscle
22	chr3:49060800-49063400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:49060800-49063600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:49060800-49063800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:49060800-49064600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:49060800-49065000	Strong transcription	Brain Anterior Caudate	brain
27	chr3:49060800-49065000	Weak transcription	Psoas Muscle	Psoas
28	chr3:49060800-49065200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:49060800-49065200	Strong transcription	Brain Angular Gyrus	brain
30	chr3:49060800-49065200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:49060800-49065400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:49060800-49065400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:49060800-49065400	Strong transcription	Fetal Stomach	stomach
34	chr3:49060800-49065600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr3:49060800-49065600	Strong transcription	Fetal Lung	lung
36	chr3:49060800-49065600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:49060800-49065800	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr3:49061000-49062000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:49061000-49062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:49061000-49062000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:49061000-49062000	Strong transcription	K562	blood
42	chr3:49061000-49062200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr3:49061000-49062200	Strong transcription	Spleen	Spleen
44	chr3:49061000-49062400	Strong transcription	Fetal Thymus	thymus
45	chr3:49061000-49062400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:49061000-49062600	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:49061000-49062600	Strong transcription	Esophagus	oesophagus
48	chr3:49061000-49062600	Genic enhancers	NHEK	skin
49	chr3:49061000-49062800	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:49061000-49062800	Genic enhancers	GM12878-XiMat	blood

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