Variant report

Variant	rs72624911
Chromosome Location	chr3:49064576-49064577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 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	NFATC1	chr3:49064555-49067398	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:49057228-49067285	MCF-7	breast:	n/a	n/a
5	MTA3	chr3:49062157-49067344	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:49057168-49067352	K562	blood:	n/a	n/a
7	POLR2A	chr3:49062416-49064578	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:49056705-49067193	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49061276-49064656	K562	blood:	n/a	n/a
10	POLR2A	chr3:49057429-49067153	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr3:49061345-49065439	K562	blood:	n/a	n/a
12	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49060280-49067138	K562	blood:	n/a	n/a
14	POLR2A	chr3:49057874-49067350	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr3:49061240-49067174	K562	blood:	n/a	n/a
16	POLR2A	chr3:49061291-49067243	HL-60	blood:	n/a	n/a
17	MTA3	chr3:49064173-49067228	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:49056596-49067347	GM12892	blood:	n/a	n/a
19	POLR2A	chr3:49063839-49064601	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:49059839-49067238	U87	brain:	n/a	n/a
21	ZNF263	chr3:49064304-49065479	HEK293-T-REx	kidney:	n/a	n/a
22	POLR2A	chr3:49061075-49067400	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr3:49061295-49064631	K562	blood:	n/a	n/a
24	POLR2A	chr3:49059865-49067325	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr3:49061791-49064598	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:49062557-49067606	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:49060152-49067239	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr3:49061352-49067178	K562	blood:	n/a	n/a
29	POLR2A	chr3:49064560-49064796	GM12878	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	chr3:49057108-49067245	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:49061177-49067268	GM12891	blood:	n/a	n/a
35	BCL3	chr3:49061823-49067340	A549	lung:	n/a	chr3:49066935-49066948 chr3:49066949-49066958 chr3:49066943-49066952 chr3:49062968-49062977
36	POLR2A	chr3:49061227-49067304	HL-60	blood:	n/a	n/a
37	POLR2A	chr3:49061116-49067257	HCT-116	colon:	n/a	n/a
38	POLR2A	chr3:49061099-49067363	U87	brain:	n/a	n/a
39	POLR2A	chr3:49061307-49067250	GM12891	blood:	n/a	n/a
40	POLR2A	chr3:49061235-49067182	HEK293	kidney:	n/a	n/a
41	POLR2A	chr3:49061594-49067530	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:49061485-49067192	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr3:49062578-49067266	PBDE	blood:	n/a	n/a
44	POLR2A	chr3:49061158-49067354	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr3:49061307-49065201	HCT-116	colon:	n/a	n/a
46	POLR2A	chr3:49060038-49067212	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr3:49061248-49067220	GM12891	blood:	n/a	n/a
48	POLR2A	chr3:49057498-49067244	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:49061776-49067196	HCT-116	colon:	n/a	n/a
50	POLR2A	chr3:49061713-49067224	GM12892	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49063329..49065224-chr3:49153770..49155924,2	K562	blood:
2	chr3:49063218..49064787-chr3:49194853..49197640,2	K562	blood:
3	chr3:49064349..49066955-chr3:49207317..49210098,3	MCF-7	breast:
4	chr3:49062158..49068430-chr3:49139884..49143886,7	K562	blood:
5	chr3:49063558..49068659-chr3:49135988..49142189,8	MCF-7	breast:
6	chr3:49062154..49067981-chr3:49128951..49132856,8	K562	blood:
7	chr3:49064325..49066470-chr3:49377582..49379875,2	K562	blood:
8	chr3:49063985..49068649-chr3:49151287..49155483,4	MCF-7	breast:
9	chr21:42692212..42695133-chr3:49064079..49066775,2	MCF-7	breast:
10	chr2:223170036..223170946-chr3:49064410..49065009,2	NB4	blood:
11	chr3:49064025..49068089-chr3:49156559..49161197,7	MCF-7	breast:
12	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
13	chr21:46493349..46495379-chr3:49062380..49065165,2	K562	blood:
14	chr20:45988079..45989634-chr3:49063562..49065359,2	MCF-7	breast:
15	chr3:49062784..49068653-chr3:49129538..49133266,11	MCF-7	breast:
16	chr3:49064195..49067148-chr3:49710210..49713126,3	MCF-7	breast:
17	chr3:49064550..49068051-chr3:49140813..49143886,3	K562	blood:

No data

Variant related genes	Relation type
IMPDH2	TF binding region
DALRD3	TF binding region
ENSG00000272434	TF binding region
ENSG00000235374	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000183844	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs34290943	1.00[ASN][1000 genomes]
rs34759087	1.00[ASN][1000 genomes]
rs61760236	1.00[ASN][1000 genomes]
rs73082331	1.00[ASN][1000 genomes]
rs73082337	1.00[ASN][1000 genomes]
rs73082363	1.00[ASN][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	chr3:49060600-49064800	Strong transcription	Brain Substantia Nigra	brain
3	chr3:49060600-49065200	Weak transcription	Small Intestine	intestine
4	chr3:49060600-49065600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49060600-49065600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:49060800-49064600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:49060800-49065000	Strong transcription	Brain Anterior Caudate	brain
8	chr3:49060800-49065000	Weak transcription	Psoas Muscle	Psoas
9	chr3:49060800-49065200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:49060800-49065200	Strong transcription	Brain Angular Gyrus	brain
11	chr3:49060800-49065200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49060800-49065400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49060800-49065400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:49060800-49065400	Strong transcription	Fetal Stomach	stomach
15	chr3:49060800-49065600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr3:49060800-49065600	Strong transcription	Fetal Lung	lung
17	chr3:49060800-49065600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:49060800-49065800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr3:49061000-49064800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:49061000-49064800	Strong transcription	Colon Smooth Muscle	Colon
21	chr3:49061000-49064800	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr3:49061000-49064800	Strong transcription	HUVEC	blood vessel
23	chr3:49061000-49064800	Strong transcription	NH-A	brain
24	chr3:49061000-49065000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:49061000-49065000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:49061000-49065000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:49061000-49065000	Strong transcription	Brain Germinal Matrix	brain
28	chr3:49061000-49065000	Strong transcription	Brain Hippocampus Middle	brain
29	chr3:49061000-49065000	Strong transcription	Fetal Intestine Small	intestine
30	chr3:49061000-49065000	Strong transcription	Fetal Kidney	kidney
31	chr3:49061000-49065000	Strong transcription	A549	lung
32	chr3:49061000-49065200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:49061000-49065200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:49061000-49065200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49061000-49065200	Strong transcription	Brain Cingulate Gyrus	brain
36	chr3:49061000-49065200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr3:49061000-49065400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:49061000-49065400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:49061000-49065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:49061000-49065600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:49061000-49065600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:49061000-49065600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:49061000-49065800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:49061000-49065800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:49061000-49066000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:49061200-49064600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:49061200-49064800	Strong transcription	Primary T cells from cord blood	blood
48	chr3:49061200-49065200	Strong transcription	Fetal Brain Female	brain
49	chr3:49061400-49064600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:49061400-49064600	Strong transcription	Ovary	ovary

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