Variant report

Variant	rs58939130
Chromosome Location	chr1:155144757-155144758
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	RCOR1	chr1:155144521-155146216	IMR90	lung:	n/a	n/a
2	MAZ	chr1:155144752-155147504	IMR90	lung:	n/a	chr1:155146251-155146266 chr1:155146974-155146983 chr1:155146252-155146262 chr1:155146252-155146261 chr1:155146253-155146262 chr1:155146978-155146987 chr1:155146253-155146263
3	POLR2A	chr1:155144504-155147249	SK-N-MC	brain:	n/a	n/a
4	MAX	chr1:155144757-155146888	A549	lung:	n/a	chr1:155146251-155146266 chr1:155146252-155146262 chr1:155146252-155146261 chr1:155146253-155146262 chr1:155146253-155146263
5	POLR2A	chr1:155144534-155144912	HepG2	liver:	n/a	n/a
6	MXI1	chr1:155144639-155149713	SK-N-SH	brain:	n/a	chr1:155146252-155146261 chr1:155146254-155146263 chr1:155146972-155146987 chr1:155146974-155146989 chr1:155146863-155146872
7	HCFC1	chr1:155144135-155146295	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155102095..155105261-chr1:155144437..155147447,3	K562	blood:
2	chr1:155056284..155060443-chr1:155143066..155147437,8	MCF-7	breast:
3	chr1:155143901..155153030-chr1:155191166..155199183,23	MCF-7	breast:
4	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
5	chr1:155144108..155147671-chr1:155293137..155296373,4	MCF-7	breast:
6	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
7	chr1:155056751..155059603-chr1:155143653..155146036,8	MCF-7	breast:
8	chr1:155021786..155024285-chr1:155144264..155145774,2	MCF-7	breast:
9	chr1:155055553..155060043-chr1:155139937..155145817,8	K562	blood:
10	chr1:155143848..155145847-chr1:155292739..155294361,2	K562	blood:
11	chr1:155105664..155110180-chr1:155143584..155151850,15	MCF-7	breast:
12	chr1:155107108..155109985-chr1:155144527..155147858,5	K562	blood:
13	chr1:155144509..155147724-chr1:155241916..155244574,3	MCF-7	breast:
14	chr1:155021809..155025289-chr1:155144477..155147497,3	K562	blood:
15	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
16	chr1:155144282..155146428-chr1:155196994..155199261,3	K562	blood:
17	chr1:155015970..155018698-chr1:155144403..155146699,2	K562	blood:

Variant related genes	Relation type
TRIM46	TF binding region
ENSG00000225855	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1611774	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154152	1.00[ASN][1000 genomes]
rs41264915	1.00[ASN][1000 genomes]
rs58925616	0.81[EUR][1000 genomes]
rs67061005	1.00[EUR][1000 genomes]
rs67579710	1.00[ASN][1000 genomes]
rs72704106	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	407 gene(s)	inside rSNPs	diseases
11	nsv8447	chr1:155144629-155156937	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155134200-155145000	Weak transcription	Small Intestine	intestine
2	chr1:155140400-155144800	Weak transcription	Psoas Muscle	Psoas
3	chr1:155142200-155144800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155142400-155144800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:155142400-155144800	Weak transcription	Gastric	stomach
6	chr1:155142400-155145000	Weak transcription	Pancreas	Pancrea
7	chr1:155142600-155145000	Weak transcription	Esophagus	oesophagus
8	chr1:155143000-155144800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:155143200-155144800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:155143200-155144800	Weak transcription	Fetal Kidney	kidney
11	chr1:155143200-155144800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:155143200-155145000	Weak transcription	Aorta	Aorta
13	chr1:155143600-155145000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155143600-155145000	Weak transcription	Ovary	ovary
15	chr1:155144000-155144800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:155144000-155144800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:155144000-155144800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:155144000-155144800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:155144200-155144800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:155144200-155144800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:155144200-155144800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:155144200-155144800	Enhancers	Liver	Liver
23	chr1:155144200-155144800	Weak transcription	Spleen	Spleen
24	chr1:155144200-155145000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:155144200-155145000	Weak transcription	Lung	lung
26	chr1:155144400-155144800	Enhancers	Adipose Nuclei	Adipose
27	chr1:155144400-155144800	Enhancers	Colon Smooth Muscle	Colon
28	chr1:155144400-155144800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:155144400-155144800	Enhancers	Fetal Intestine Large	intestine
30	chr1:155144400-155144800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr1:155144400-155144800	Enhancers	Fetal Stomach	stomach
32	chr1:155144400-155144800	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr1:155144400-155144800	Transcr. at gene 5' and 3'	K562	blood
34	chr1:155144400-155145000	Enhancers	Primary T cells from cord blood	blood
35	chr1:155144400-155145000	Enhancers	Primary hematopoietic stem cells	blood
36	chr1:155144400-155145000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:155144400-155145000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:155144400-155145000	Enhancers	Fetal Heart	heart
39	chr1:155144400-155145200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:155144400-155145200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:155144600-155144800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr1:155144600-155144800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr1:155144600-155144800	Enhancers	H9 Cell Line	embryonic stem cell
44	chr1:155144600-155144800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:155144600-155144800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr1:155144600-155144800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr1:155144600-155144800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:155144600-155144800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr1:155144600-155144800	Enhancers	Brain Angular Gyrus	brain
50	chr1:155144600-155144800	Enhancers	Brain Cingulate Gyrus	brain

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