Variant report

Variant	rs58284360
Chromosome Location	chr3:53915623-53915624
allele	C/T
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	SMC3	chr3:53915550-53916266	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:53915603-53915912	HCT-116	colon:	n/a	n/a
3	MXI1	chr3:53914153-53917137	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:53915590-53916354	K562	blood:	n/a	n/a
5	BCLAF1	chr3:53915471-53916369	GM12878	blood:	n/a	chr3:53915953-53915962
6	POLR2A	chr3:53915529-53916476	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELF1	chr3:53915497-53916386	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:53915582-53916339	K562	blood:	n/a	n/a
9	YY1	chr3:53915315-53916620	SK-N-SH	brain:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
10	POLR2A	chr3:53915613-53916332	A549	lung:	n/a	n/a
11	POLR2A	chr3:53915551-53916460	GM12878	blood:	n/a	n/a
12	MAX	chr3:53915587-53916412	ECC-1	luminal epithelium:	n/a	chr3:53915928-53915938
13	POLR2A	chr3:53915579-53916566	Hela-S3	cervix:	n/a	n/a
14	RUNX3	chr3:53915482-53916459	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:53915591-53916455	MCF-7	breast:	n/a	n/a
16	WRNIP1	chr3:53915593-53916076	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:53915606-53916431	HEK293	kidney:	n/a	n/a
18	POLR2A	chr3:53915584-53916449	HL-60	blood:	n/a	n/a
19	YY1	chr3:53915503-53916558	GM12878	blood:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
20	MAZ	chr3:53915007-53917351	IMR90	lung:	n/a	chr3:53915928-53915938
21	UBTF	chr3:53915609-53916313	K562	blood:	n/a	n/a
22	RUNX3	chr3:53915515-53916434	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:53915480-53916411	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:53915616-53916346	GM10847	blood:	n/a	n/a
25	GABPA	chr3:53915503-53916419	MCF-7	breast:	n/a	chr3:53916196-53916210 chr3:53916199-53916208 chr3:53916199-53916210 chr3:53916301-53916310
26	POLR2A	chr3:53915493-53917518	GM12891	blood:	n/a	n/a
27	POLR2A	chr3:53915552-53916515	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr3:53915552-53916354	K562	blood:	n/a	n/a
29	POLR2A	chr3:53915574-53916547	GM15510	blood:	n/a	n/a
30	TAF1	chr3:53915416-53916456	H1-neurons	neurons:	n/a	n/a
31	SIN3AK20	chr3:53915509-53916291	MCF-7	breast:	n/a	n/a
32	YY1	chr3:53915544-53916573	K562	blood:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
33	POLR2A	chr3:53915466-53916563	H1-neurons	neurons:	n/a	n/a
34	TBL1XR1	chr3:53915550-53915843	K562	blood:	n/a	n/a
35	POLR2A	chr3:53915576-53916541	GM12892	blood:	n/a	n/a
36	GABPA	chr3:53915587-53916479	SK-N-SH	brain:	n/a	chr3:53916196-53916210 chr3:53916199-53916208 chr3:53916199-53916210 chr3:53916301-53916310
37	POLR2A	chr3:53915492-53917996	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr3:53915549-53916281	Hela-S3	cervix:	n/a	n/a
39	CREB1	chr3:53915523-53916578	HepG2	liver:	n/a	n/a
40	TAF1	chr3:53915586-53916386	HepG2	liver:	n/a	n/a
41	YY1	chr3:53915602-53916545	SK-N-SH_RA	brain:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
42	RELA	chr3:53915572-53916515	GM15510	blood:	n/a	n/a
43	MAX	chr3:53915552-53916449	HepG2	liver:	n/a	chr3:53915928-53915938
44	POLR2A	chr3:53915558-53916518	GM19193	blood:	n/a	n/a
45	POLR2A	chr3:53915604-53916813	GM12878	blood:	n/a	n/a
46	MXI1	chr3:53914895-53916494	IMR90	lung:	n/a	n/a
47	YY1	chr3:53915547-53916507	GM12891	blood:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
48	POLR2A	chr3:53915564-53916691	GM18951	blood:	n/a	n/a
49	POLR2A	chr3:53915622-53916319	K562	blood:	n/a	n/a
50	POLR2A	chr3:53915529-53916509	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
3	chr3:53906924..53910795-chr3:53914021..53916121,3	MCF-7	breast:
4	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
5	chr3:53915297..53916473-chr3:53925441..53926286,3	MCF-7	breast:
6	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
7	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:
8	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

Variant related genes	Relation type
ACTR8	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000113811	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2304574	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58746828	0.90[AFR][1000 genomes]
rs6774651	0.89[AFR][1000 genomes]
rs6798958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9810568	0.90[AFR][1000 genomes]
rs9873491	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53914600-53915800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr3:53914800-53915800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:53914800-53915800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:53914800-53916600	Active TSS	Fetal Muscle Trunk	muscle
5	chr3:53915000-53915800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr3:53915000-53915800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr3:53915000-53915800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr3:53915000-53915800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:53915000-53916000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr3:53915000-53916800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:53915200-53915800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr3:53915200-53915800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr3:53915200-53915800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:53915200-53915800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:53915200-53916200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:53915200-53916400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:53915200-53916400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:53915200-53916400	Active TSS	Psoas Muscle	Psoas
19	chr3:53915200-53916600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:53915200-53916600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:53915200-53916600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:53915200-53916600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:53915200-53916600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr3:53915200-53916600	Active TSS	Aorta	Aorta
25	chr3:53915200-53916600	Active TSS	Fetal Intestine Small	intestine
26	chr3:53915200-53916600	Active TSS	Left Ventricle	heart
27	chr3:53915200-53916600	Active TSS	Lung	lung
28	chr3:53915200-53916600	Active TSS	Pancreas	Pancrea
29	chr3:53915200-53916600	Active TSS	A549	lung
30	chr3:53915200-53916600	Active TSS	NHDF-Ad	bronchial
31	chr3:53915200-53916600	Active TSS	NHLF	lung
32	chr3:53915200-53916800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:53915200-53916800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:53915200-53916800	Active TSS	Fetal Brain Male	brain
35	chr3:53915200-53916800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr3:53915400-53915800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr3:53915400-53915800	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr3:53915400-53916000	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr3:53915400-53916200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:53915400-53916200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:53915400-53916400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:53915400-53916400	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:53915400-53916400	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr3:53915400-53916400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:53915400-53916400	Active TSS	Brain Cingulate Gyrus	brain
46	chr3:53915400-53916400	Active TSS	Brain Hippocampus Middle	brain
47	chr3:53915400-53916400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr3:53915400-53916400	Active TSS	Brain Substantia Nigra	brain
49	chr3:53915400-53916400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr3:53915400-53916400	Active TSS	Fetal Heart	heart

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