Variant report

Variant	rs8024550
Chromosome Location	chr15:45670681-45670682
allele	A/C
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	POLR2A	chr15:45669585-45671424	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:45670453-45671303	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:45670238-45671169	GM18951	blood:	n/a	n/a
4	USF1	chr15:45670436-45670920	GM12878	blood:	n/a	n/a
5	USF1	chr15:45670381-45671033	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr15:45670204-45670808	MCF-7	breast:	n/a	n/a
7	POLR2A	chr15:45670063-45671360	GM12891	blood:	n/a	n/a
8	FOS	chr15:45670340-45670731	HUVEC	blood vessel:	n/a	chr15:45670539-45670550 chr15:45670540-45670550
9	TBP	chr15:45670525-45671286	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:45670236-45671387	GM12891	blood:	n/a	n/a
11	USF2	chr15:45670352-45671289	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:45670164-45671378	GM12892	blood:	n/a	n/a
13	CTCF	chr15:45670053-45670857	A549	lung:	n/a	chr15:45670304-45670317
14	EP300	chr15:45670514-45670714	GM12878	blood:	n/a	chr15:45670523-45670532
15	CTCF	chr15:45670295-45670739	GM12878	blood:	n/a	chr15:45670304-45670317
16	E2F6	chr15:45669921-45671050	H1-hESC	embryonic stem cell:	n/a	n/a
17	SRF	chr15:45670664-45671072	H1-hESC	embryonic stem cell:	n/a	chr15:45670830-45670840 chr15:45670902-45670920 chr15:45670848-45670865
18	POLR2A	chr15:45670322-45670924	SK-N-MC	brain:	n/a	n/a
19	ZNF143	chr15:45670145-45671311	GM12878	blood:	n/a	n/a
20	MAX	chr15:45670092-45671019	A549	lung:	n/a	n/a
21	POLR2A	chr15:45668632-45671831	GM12891	blood:	n/a	n/a
22	POLR2A	chr15:45669657-45671407	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr15:45670233-45671264	GM12878	blood:	n/a	n/a
24	MAX	chr15:45669945-45671072	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr15:45670269-45670877	A549	lung:	n/a	n/a
26	MYC	chr15:45670346-45671267	H1-hESC	embryonic stem cell:	n/a	n/a
27	SP1	chr15:45670502-45671005	GM12878	blood:	n/a	n/a
28	NFYB	chr15:45670348-45671047	GM12878	blood:	n/a	n/a
29	POU2F2	chr15:45670466-45671329	GM12878	blood:	n/a	chr15:45671073-45671086 chr15:45671037-45671059 chr15:45671076-45671090 chr15:45671074-45671092 chr15:45671037-45671058 chr15:45671073-45671086 chr15:45671073-45671086 chr15:45671079-45671088
30	SRF	chr15:45670622-45671054	GM12878	blood:	n/a	chr15:45670830-45670840 chr15:45670902-45670920 chr15:45670848-45670865
31	FOSL2	chr15:45670309-45670741	SK-N-SH	brain:	n/a	chr15:45670540-45670550
32	CTCF	chr15:45669802-45670965	SK-N-SH	brain:	n/a	chr15:45669966-45669979 chr15:45670304-45670317
33	POLR2A	chr15:45670409-45671389	GM12891	blood:	n/a	n/a
34	JUND	chr15:45670256-45670760	H1-hESC	embryonic stem cell:	n/a	chr15:45670540-45670550 chr15:45670277-45670286
35	SIN3A	chr15:45669548-45671311	H1-hESC	embryonic stem cell:	n/a	chr15:45670385-45670396 chr15:45670390-45670399
36	POLR2A	chr15:45669821-45671034	GM12878	blood:	n/a	n/a
37	USF1	chr15:45670381-45670955	SK-N-SH_RA	brain:	n/a	n/a
38	POLR2A	chr15:45670238-45671315	GM15510	blood:	n/a	n/a
39	YY1	chr15:45670214-45670947	GM12892	blood:	n/a	chr15:45670281-45670295 chr15:45670873-45670887 chr15:45670872-45670883 chr15:45670872-45670881 chr15:45670278-45670287 chr15:45670281-45670290
40	TCF3	chr15:45670204-45671041	GM12878	blood:	n/a	chr15:45670817-45670830
41	POLR2A	chr15:45669723-45671394	GM12891	blood:	n/a	n/a
42	POLR2A	chr15:45670211-45671287	GM12892	blood:	n/a	n/a
43	POLR2A	chr15:45670351-45670968	A549	lung:	n/a	n/a
44	ZNF263	chr15:45669901-45670971	HEK293-T-REx	kidney:	n/a	n/a
45	PAX5	chr15:45670410-45670934	GM12892	blood:	n/a	n/a
46	POLR2A	chr15:45670202-45671056	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:45670358-45671139	GM18526	blood:	n/a	n/a
48	FOSL2	chr15:45670305-45670725	MCF-7	breast:	n/a	chr15:45670540-45670550
49	CHD2	chr15:45670092-45671253	GM12878	blood:	n/a	n/a
50	MAX	chr15:45670053-45671275	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45670316..45671297-chr6:86353473..86353980,2	Hela-S3	cervix:

Variant related genes	Relation type
GATM	TF binding region
ENSG00000135316	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1055395	0.83[AMR][1000 genomes]
rs1145072	0.83[AMR][1000 genomes]
rs1145073	0.83[AMR][1000 genomes]
rs1145075	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1145082	0.83[AMR][1000 genomes]
rs1145095	0.81[AMR][1000 genomes]
rs1145096	0.81[AMR][1000 genomes]
rs1145099	0.81[AMR][1000 genomes]
rs1153833	0.81[AMR][1000 genomes]
rs1153848	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1153850	0.83[AMR][1000 genomes]
rs1153851	0.83[AMR][1000 genomes]
rs1153856	0.83[AMR][1000 genomes]
rs1346265	0.83[AMR][1000 genomes]
rs1706800	0.81[AMR][1000 genomes]
rs1706801	0.81[AMR][1000 genomes]
rs1706802	0.81[AMR][1000 genomes]
rs1719248	0.81[AMR][1000 genomes]
rs1834686	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1874318	0.83[AMR][1000 genomes]
rs2217121	0.83[AMR][1000 genomes]
rs2413765	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2433605	0.83[AMR][1000 genomes]
rs2433606	0.83[AMR][1000 genomes]
rs2433609	0.83[AMR][1000 genomes]
rs2453544	0.83[AMR][1000 genomes]
rs2453547	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2461704	0.83[AMR][1000 genomes]
rs2467850	0.94[AFR][1000 genomes]
rs2467852	0.83[AMR][1000 genomes]
rs2467856	0.83[AMR][1000 genomes]
rs2467857	0.83[AMR][1000 genomes]
rs2467859	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2486271	0.83[AMR][1000 genomes]
rs2486289	0.83[AMR][1000 genomes]
rs2486290	0.83[AMR][1000 genomes]
rs2789612	0.81[AMR][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 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	chr15:45668400-45671200	Bivalent/Poised TSS	Fetal Kidney	kidney
2	chr15:45669000-45671200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:45669000-45671200	Active TSS	Ovary	ovary
4	chr15:45669000-45671200	Active TSS	Right Atrium	heart
5	chr15:45669000-45671600	Active TSS	Brain Angular Gyrus	brain
6	chr15:45669000-45671800	Active TSS	Pancreas	Pancrea
7	chr15:45669200-45670800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr15:45669200-45671200	Active TSS	Brain Anterior Caudate	brain
9	chr15:45669200-45671200	Active TSS	Brain Hippocampus Middle	brain
10	chr15:45669200-45671400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr15:45669400-45671200	Active TSS	Brain Substantia Nigra	brain
12	chr15:45669400-45671400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr15:45669400-45675200	Weak transcription	HepG2	liver
14	chr15:45669600-45671000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:45669600-45671000	Active TSS	Brain Cingulate Gyrus	brain
16	chr15:45669600-45671200	Active TSS	Colon Smooth Muscle	Colon
17	chr15:45669600-45671400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr15:45669600-45671400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr15:45669600-45671400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr15:45669600-45671400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr15:45669600-45671400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr15:45669600-45671400	Active TSS	Aorta	Aorta
23	chr15:45669600-45671400	Active TSS	Brain Germinal Matrix	brain
24	chr15:45669600-45671600	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr15:45669600-45671800	Active TSS	Left Ventricle	heart
26	chr15:45669800-45671000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:45669800-45671000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
28	chr15:45669800-45671000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:45669800-45671200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:45669800-45671200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr15:45669800-45671200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr15:45669800-45671200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr15:45669800-45671200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:45669800-45671200	Bivalent/Poised TSS	NHLF	lung
35	chr15:45669800-45671400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr15:45669800-45671400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr15:45669800-45671400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:45669800-45671400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:45669800-45671400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:45669800-45671400	Active TSS	Esophagus	oesophagus
41	chr15:45669800-45671400	Active TSS	Psoas Muscle	Psoas
42	chr15:45669800-45671400	Active TSS	Rectal Smooth Muscle	rectum
43	chr15:45669800-45671400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr15:45670000-45670800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:45670000-45670800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:45670000-45671000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:45670000-45671000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:45670000-45671000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:45670000-45671000	Active TSS	Fetal Brain Female	brain
50	chr15:45670000-45671200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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