Variant report

Variant	rs60523415
Chromosome Location	chr3:150477002-150477003
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	POLR2A	chr3:150476883-150483109	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:150476868-150477610	GM12878	blood:	n/a	n/a
3	FOS	chr3:150476853-150477406	MCF10A-Er-Src	breast:	n/a	chr3:150477201-150477213
4	WRNIP1	chr3:150477002-150478876	GM12878	blood:	n/a	n/a
5	FOS	chr3:150476830-150477444	MCF10A-Er-Src	breast:	n/a	chr3:150477201-150477213
6	JUND	chr3:150476834-150477055	HepG2	liver:	n/a	chr3:150476947-150476958
7	POLR2A	chr3:150476869-150478332	HepG2	liver:	n/a	n/a
8	NR2F2	chr3:150476762-150478075	MCF-7	breast:	n/a	n/a
9	CEBPB	chr3:150476928-150477473	MCF-7	breast:	n/a	chr3:150477059-150477076 chr3:150477060-150477071
10	POLR2A	chr3:150476793-150477541	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:150476896-150484835	GM12878	blood:	n/a	n/a
12	FOS	chr3:150476926-150477443	MCF10A-Er-Src	breast:	n/a	chr3:150477201-150477213
13	FOSL2	chr3:150476809-150477548	MCF-7	breast:	n/a	chr3:150477201-150477213
14	POLR2A	chr3:150476950-150483136	PBDE	blood:	n/a	n/a
15	POLR2A	chr3:150476862-150478743	HepG2	liver:	n/a	n/a
16	GATA3	chr3:150476857-150477607	MCF-7	breast:	n/a	chr3:150477532-150477543
17	POLR2A	chr3:150476072-150477396	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:150127920..150130058-chr3:150474228..150477225,3	MCF-7	breast:
2	chr3:150379555..150382214-chr3:150476705..150479002,2	K562	blood:
3	chr3:150447677..150449364-chr3:150475265..150477191,2	K562	blood:
4	chr17:57920099..57922060-chr3:150475715..150477426,2	MCF-7	breast:
5	chr3:150476989..150478844-chr3:150495018..150496645,2	MCF-7	breast:
6	chr3:150319591..150322535-chr3:150472919..150477532,4	MCF-7	breast:
7	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:

Variant related genes	Relation type
SIAH2-AS1	TF binding region
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000244668	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1373418	0.81[EUR][1000 genomes]
rs1444197	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16862842	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814463	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1814464	0.81[EUR][1000 genomes]
rs1838337	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1879420	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1915365	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2014279	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2018246	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2116684	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2120596	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34348847	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34771595	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851356	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41354246	0.81[EUR][1000 genomes]
rs41372346	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41454348	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56840421	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57278175	0.93[EUR][1000 genomes]
rs57359526	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57869178	0.81[EUR][1000 genomes]
rs57965761	0.86[AMR][1000 genomes]
rs58403524	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58418105	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60092981	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60259684	0.81[EUR][1000 genomes]
rs60538652	0.91[AMR][1000 genomes]
rs61628582	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6440696	0.81[EUR][1000 genomes]
rs6440697	0.81[EUR][1000 genomes]
rs6440698	0.81[EUR][1000 genomes]
rs6769917	0.81[EUR][1000 genomes]
rs6777178	0.81[EUR][1000 genomes]
rs6795396	0.93[EUR][1000 genomes]
rs6803830	1.00[EUR][1000 genomes]
rs6805481	0.81[EUR][1000 genomes]
rs6806197	0.93[EUR][1000 genomes]
rs71764080	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72993403	0.86[EUR][1000 genomes]
rs73003787	0.93[EUR][1000 genomes]
rs73003792	0.81[EUR][1000 genomes]
rs73006998	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73010941	0.81[EUR][1000 genomes]
rs73010947	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73010956	0.81[EUR][1000 genomes]
rs73010964	0.81[EUR][1000 genomes]
rs73010965	0.81[EUR][1000 genomes]
rs73010967	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73869297	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7615125	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615292	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617507	0.81[EUR][1000 genomes]
rs7628481	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628776	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150453800-150478000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:150454600-150477200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:150456400-150477600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:150456600-150477600	Weak transcription	Fetal Brain Male	brain
5	chr3:150456800-150477400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:150457000-150478800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:150457600-150477600	Weak transcription	HUVEC	blood vessel
8	chr3:150459000-150477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:150460200-150477600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:150460400-150477600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:150463000-150477800	Weak transcription	NH-A	brain
12	chr3:150463000-150478400	Weak transcription	HSMM	muscle
13	chr3:150463200-150477600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:150466200-150477600	Weak transcription	Aorta	Aorta
15	chr3:150466400-150477800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:150466800-150477600	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:150467000-150477600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:150467000-150477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:150467400-150477200	Weak transcription	NHDF-Ad	bronchial
20	chr3:150467400-150477600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:150470000-150477600	Weak transcription	Fetal Lung	lung
22	chr3:150470000-150477800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:150470000-150478800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:150470200-150477400	Weak transcription	Primary T cells from cord blood	blood
25	chr3:150470200-150477600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:150470200-150477800	Weak transcription	Right Ventricle	heart
27	chr3:150470600-150477800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:150471200-150477200	Weak transcription	Psoas Muscle	Psoas
29	chr3:150471200-150477200	Weak transcription	Spleen	Spleen
30	chr3:150471200-150477400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:150471200-150479600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:150471400-150477200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:150471400-150477800	Weak transcription	HSMMtube	muscle
34	chr3:150471600-150477600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:150471600-150477600	Weak transcription	Esophagus	oesophagus
36	chr3:150471600-150479600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:150472200-150477200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:150472200-150477600	Weak transcription	Lung	lung
39	chr3:150473800-150478200	Enhancers	Fetal Heart	heart
40	chr3:150474000-150477200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:150474000-150478000	Enhancers	Stomach Mucosa	stomach
42	chr3:150474000-150478800	Enhancers	Small Intestine	intestine
43	chr3:150474200-150477200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr3:150474200-150477200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:150474400-150477200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:150474400-150477200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:150474400-150477800	Genic enhancers	K562	blood
48	chr3:150474600-150477200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:150474600-150477200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:150474600-150477800	Strong transcription	Fetal Stomach	stomach

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