Variant report

Variant	rs61542554
Chromosome Location	chr2:47080013-47080014
allele	C/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	chr2:47079569-47080296	SK-N-SH	brain:	n/a	n/a
2	TAL1	chr2:47079877-47080014	K562	blood:	n/a	n/a
3	CEBPB	chr2:47079591-47080081	K562	blood:	n/a	n/a
4	RCOR1	chr2:47079872-47080212	K562	blood:	n/a	n/a
5	CEBPB	chr2:47079976-47080072	Hela-S3	cervix:	n/a	n/a
6	EP300	chr2:47079733-47080069	K562	blood:	n/a	n/a
7	ZNF384	chr2:47079576-47080149	K562	blood:	n/a	n/a
8	POLR2A	chr2:47079715-47080065	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr2:47079492-47080355	SK-N-SH	brain:	n/a	n/a
10	JUND	chr2:47079757-47080023	K562	blood:	n/a	n/a
11	FOS	chr2:47079714-47080045	HUVEC	blood vessel:	n/a	chr2:47079858-47079869
12	STAT3	chr2:47079996-47080365	MCF10A-Er-Src	breast:	n/a	n/a
13	FOSL2	chr2:47079579-47080101	SK-N-SH	brain:	n/a	n/a
14	FOS	chr2:47079758-47080269	MCF10A-Er-Src	breast:	n/a	chr2:47079858-47079869
15	MAFK	chr2:47079745-47080290	K562	blood:	n/a	n/a
16	RFX5	chr2:47079916-47080108	K562	blood:	n/a	n/a
17	MAFF	chr2:47079735-47080031	K562	blood:	n/a	n/a
18	FOS	chr2:47079848-47080048	MCF10A-Er-Src	breast:	n/a	chr2:47079858-47079869

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47072318..47075227-chr2:47078987..47080534,2	K562	blood:
2	chr2:47077957..47080077-chr2:47082546..47084432,2	K562	blood:

Variant related genes	Relation type
LINC01119	TF binding region
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13415138	0.86[AMR][1000 genomes]
rs4953431	0.91[EUR][1000 genomes]
rs4953434	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72804479	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875343	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935380	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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	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
2	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
3	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
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47069400-47082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:47072600-47080400	Enhancers	HMEC	breast
3	chr2:47072800-47080200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47072800-47080400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:47075200-47080400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:47075200-47084400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:47076600-47081600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:47076800-47081600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:47077000-47080600	Enhancers	K562	blood
10	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:47077400-47081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:47077600-47081600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:47077600-47081600	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:47077600-47081600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:47078000-47080200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:47078000-47080400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:47078000-47080400	Enhancers	NH-A	brain
18	chr2:47078000-47081600	Weak transcription	Esophagus	oesophagus
19	chr2:47078000-47082000	Weak transcription	Small Intestine	intestine
20	chr2:47078000-47083400	Weak transcription	Fetal Intestine Large	intestine
21	chr2:47078000-47085200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:47078000-47085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:47078200-47081400	Weak transcription	Adipose Nuclei	Adipose
24	chr2:47078200-47081600	Weak transcription	Fetal Lung	lung
25	chr2:47078200-47081600	Weak transcription	Spleen	Spleen
26	chr2:47078400-47080800	Weak transcription	Left Ventricle	heart
27	chr2:47078400-47081000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:47078400-47081400	Weak transcription	HSMMtube	muscle
29	chr2:47078400-47081600	Weak transcription	Colonic Mucosa	Colon
30	chr2:47078400-47081600	Weak transcription	Fetal Heart	heart
31	chr2:47078400-47081600	Weak transcription	Lung	lung
32	chr2:47078400-47081600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:47078400-47081600	Weak transcription	Right Ventricle	heart
34	chr2:47078400-47083200	Weak transcription	Psoas Muscle	Psoas
35	chr2:47078600-47081200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:47078600-47081400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:47078600-47081400	Weak transcription	Fetal Stomach	stomach
38	chr2:47078600-47081600	Weak transcription	Aorta	Aorta
39	chr2:47078600-47081600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:47078600-47081600	Weak transcription	Ovary	ovary
41	chr2:47078600-47081600	Weak transcription	Right Atrium	heart
42	chr2:47078600-47081600	Weak transcription	HSMM	muscle
43	chr2:47078600-47082000	Weak transcription	Stomach Mucosa	stomach
44	chr2:47078600-47082600	Weak transcription	Pancreas	Pancrea
45	chr2:47079200-47080200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:47079200-47080400	Enhancers	Hela-S3	cervix
47	chr2:47079200-47081400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:47079200-47082600	Enhancers	HUVEC	blood vessel
49	chr2:47079400-47080200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:47079400-47080800	Weak transcription	Stomach Smooth Muscle	stomach

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