Variant report

Variant	rs72804446
Chromosome Location	chr2:47039315-47039316
allele	A/G
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	GATA3	chr2:47039121-47040635	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:47038886-47040804	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr2:47039138-47040781	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr2:47038968-47040824	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr2:47039144-47040410	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr2:47039215-47040687	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr2:47039134-47040716	SK-N-SH	brain:	n/a	n/a
8	EP300	chr2:47039184-47040749	SK-N-SH_RA	brain:	n/a	chr2:47039929-47039943
9	EP300	chr2:47039047-47040563	SK-N-SH_RA	brain:	n/a	chr2:47039929-47039943
10	SP1	chr2:47039196-47040179	A549	lung:	n/a	chr2:47039294-47039301
11	TCF12	chr2:47039076-47040890	SK-N-SH	brain:	n/a	chr2:47039504-47039512 chr2:47039262-47039270
12	RAD21	chr2:47039259-47040516	SK-N-SH_RA	brain:	n/a	chr2:47039275-47039284 chr2:47039328-47039338
13	TCF12	chr2:47039101-47040929	SK-N-SH	brain:	n/a	chr2:47039504-47039512 chr2:47039262-47039270
14	RXRA	chr2:47038999-47040683	SK-N-SH	brain:	n/a	chr2:47039439-47039455
15	RXRA	chr2:47039178-47040202	SK-N-SH	brain:	n/a	chr2:47039439-47039455
16	TEAD4	chr2:47039118-47040521	SK-N-SH	brain:	n/a	n/a
17	EP300	chr2:47037776-47041932	SK-N-SH	brain:	n/a	chr2:47041533-47041547 chr2:47038862-47038876 chr2:47039929-47039943
18	POLR2A	chr2:47039304-47040491	SK-N-SH	brain:	n/a	n/a
19	GATA3	chr2:47039113-47040781	SK-N-SH	brain:	n/a	n/a
20	RAD21	chr2:47039241-47040627	SK-N-SH_RA	brain:	n/a	chr2:47039275-47039284 chr2:47039328-47039338
21	EP300	chr2:47039029-47040807	SK-N-SH	brain:	n/a	chr2:47039929-47039943
22	EP300	chr2:47039069-47040473	SK-N-SH	brain:	n/a	chr2:47039929-47039943

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47038370..47041063-chr2:47049130..47051492,2	K562	blood:

Variant related genes	Relation type
LINC01119	TF binding region
LINC01118	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17035709	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17824594	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55980660	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56060227	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56172110	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58979440	0.91[ASN][1000 genomes]
rs72804436	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72804437	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72804438	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72804445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72804451	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72804452	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72804458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72804469	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72804470	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47031400-47043600	Weak transcription	Spleen	Spleen
2	chr2:47031400-47052000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47034400-47039400	Weak transcription	HUVEC	blood vessel
4	chr2:47034400-47039400	Weak transcription	NHEK	skin
5	chr2:47034400-47039600	Weak transcription	HMEC	breast
6	chr2:47037600-47042400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:47038000-47039400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:47038000-47039400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:47038000-47039400	Enhancers	NHLF	lung
10	chr2:47038000-47042600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:47038200-47042400	Enhancers	Fetal Stomach	stomach
12	chr2:47038200-47042600	Enhancers	NHDF-Ad	bronchial
13	chr2:47038200-47042800	Enhancers	Colon Smooth Muscle	Colon
14	chr2:47038400-47039400	Enhancers	Osteobl	bone
15	chr2:47038400-47039800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr2:47038400-47040600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr2:47038400-47041400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:47038400-47041600	Enhancers	Fetal Lung	lung
19	chr2:47038600-47039400	Enhancers	A549	lung
20	chr2:47038600-47039400	Enhancers	HSMMtube	muscle
21	chr2:47038600-47039400	Enhancers	NH-A	brain
22	chr2:47038600-47039800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr2:47038600-47042000	Enhancers	Brain Anterior Caudate	brain
24	chr2:47038600-47042000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:47038600-47042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:47038600-47042400	Enhancers	Fetal Muscle Leg	muscle
27	chr2:47038600-47042400	Enhancers	Ovary	ovary
28	chr2:47038600-47042400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:47038600-47042600	Enhancers	Rectal Smooth Muscle	rectum
30	chr2:47038600-47042600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:47038600-47042800	Enhancers	Left Ventricle	heart
32	chr2:47038600-47046400	Enhancers	Lung	lung
33	chr2:47038600-47046400	Enhancers	Right Atrium	heart
34	chr2:47038800-47039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:47038800-47039400	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:47038800-47039400	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:47038800-47040200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:47038800-47041800	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:47038800-47042800	Enhancers	Fetal Heart	heart
40	chr2:47038800-47043800	Enhancers	Placenta	Placenta
41	chr2:47038800-47044000	Weak transcription	Esophagus	oesophagus
42	chr2:47038800-47046200	Enhancers	Right Ventricle	heart
43	chr2:47039000-47039400	Enhancers	Brain Hippocampus Middle	brain
44	chr2:47039000-47039400	Enhancers	Small Intestine	intestine
45	chr2:47039000-47039400	Enhancers	HSMM	muscle
46	chr2:47039000-47040400	Enhancers	Brain Germinal Matrix	brain
47	chr2:47039200-47039400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:47039200-47039400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:47039200-47039400	Enhancers	Fetal Intestine Large	intestine
50	chr2:47039200-47039400	Enhancers	Fetal Thymus	thymus

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