Variant report

Variant	rs58684123
Chromosome Location	chr3:139255452-139255453
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	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr3:139255423-139256797	HEK293	kidney:	n/a	chr3:139256358-139256367 chr3:139256355-139256364
3	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365

No.	Distal block	Cell Line	Cell type
1	chr3:139253381..139256319-chr3:139269568..139271702,2	MCF-7	breast:
2	chr3:139239944..139241919-chr3:139253042..139255747,2	MCF-7	breast:
3	chr3:139251496..139253555-chr3:139254279..139256942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248932	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11914638	0.87[ASN][1000 genomes]
rs35847383	0.81[ASN][1000 genomes]
rs57253122	0.94[ASN][1000 genomes]
rs59610262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622961	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139249600-139256400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139249800-139257400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:139250000-139256600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:139250600-139256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:139251000-139255800	Enhancers	Fetal Kidney	kidney
7	chr3:139251200-139255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
9	chr3:139251400-139256400	Enhancers	Liver	Liver
10	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
11	chr3:139251600-139255800	Enhancers	Fetal Brain Male	brain
12	chr3:139251600-139256400	Enhancers	HMEC	breast
13	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
14	chr3:139252000-139257600	Enhancers	Left Ventricle	heart
15	chr3:139252200-139257600	Enhancers	Brain Substantia Nigra	brain
16	chr3:139252400-139256200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:139252600-139255800	Enhancers	Right Atrium	heart
18	chr3:139252800-139255800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:139252800-139257600	Enhancers	Right Ventricle	heart
20	chr3:139252800-139257800	Weak transcription	Psoas Muscle	Psoas
21	chr3:139253000-139258000	Weak transcription	Small Intestine	intestine
22	chr3:139253000-139258200	Enhancers	Spleen	Spleen
23	chr3:139253400-139257400	Genic enhancers	Fetal Stomach	stomach
24	chr3:139253600-139257400	Enhancers	Brain Hippocampus Middle	brain
25	chr3:139253800-139256000	Enhancers	HSMMtube	muscle
26	chr3:139253800-139256400	Enhancers	NHEK	skin
27	chr3:139253800-139256600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:139253800-139257600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr3:139254200-139255800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:139254400-139255600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:139254400-139255600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:139254400-139255800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:139254400-139256400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:139254400-139256800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:139254600-139255800	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr3:139254600-139255800	Genic enhancers	Fetal Muscle Leg	muscle
37	chr3:139254600-139256400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:139254600-139256600	Genic enhancers	Fetal Lung	lung
39	chr3:139254600-139256800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:139254600-139257400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:139254800-139255600	Genic enhancers	NH-A	brain
42	chr3:139254800-139256200	Weak transcription	Adipose Nuclei	Adipose
43	chr3:139254800-139256400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:139254800-139256800	Weak transcription	Esophagus	oesophagus
45	chr3:139254800-139257200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:139255000-139256000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr3:139255000-139256000	Weak transcription	HepG2	liver
48	chr3:139255000-139256200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:139255000-139256200	Genic enhancers	Pancreas	Pancrea
50	chr3:139255000-139257800	Weak transcription	HSMM	muscle

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