Variant report

Variant	rs2560040
Chromosome Location	chr5:154209207-154209208
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	MYC	chr5:154208771-154209850	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr5:154209004-154210075	MCF-7	breast:	n/a	n/a
3	TCF7L2	chr5:154209099-154209838	MCF-7	breast:	n/a	chr5:154209533-154209542 chr5:154209530-154209544 chr5:154209535-154209542
4	STAT3	chr5:154208922-154209963	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr5:154208886-154209218	K562	blood:	n/a	n/a
6	NR2F2	chr5:154209148-154210006	MCF-7	breast:	n/a	n/a
7	STAT3	chr5:154209054-154209971	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr5:154208816-154209475	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr5:154209004-154210012	MCF-7	breast:	n/a	chr5:154209623-154209630
10	JUND	chr5:154208927-154210227	HCT-116	colon:	n/a	n/a
11	HDAC2	chr5:154209172-154209978	MCF-7	breast:	n/a	n/a
12	POLR2A	chr5:154208631-154209775	SK-N-MC	brain:	n/a	n/a
13	RAD21	chr5:154208768-154209318	MCF-7	breast:	n/a	n/a
14	E2F4	chr5:154208936-154209414	MCF10A-Er-Src	breast:	n/a	n/a
15	FOSL2	chr5:154209172-154209886	MCF-7	breast:	n/a	n/a
16	FOS	chr5:154209122-154209895	MCF10A-Er-Src	breast:	n/a	n/a
17	SIN3AK20	chr5:154208578-154210128	MCF-7	breast:	n/a	n/a
18	FOSL1	chr5:154208908-154210102	HCT-116	colon:	n/a	n/a
19	GATA3	chr5:154208702-154210005	MCF-7	breast:	n/a	chr5:154208978-154208988
20	MYC	chr5:154209133-154210455	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr5:154208637-154209924	MCF-7	breast:	n/a	n/a
22	POLR2A	chr5:154209111-154209562	K562	blood:	n/a	n/a
23	STAT3	chr5:154209098-154209939	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr5:154209027-154209914	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr5:154209077-154209873	MCF10A-Er-Src	breast:	n/a	n/a
26	JUND	chr5:154208942-154210058	HCT-116	colon:	n/a	n/a
27	TCF12	chr5:154209197-154210016	MCF-7	breast:	n/a	chr5:154209623-154209630
28	SIN3AK20	chr5:154209136-154209906	MCF-7	breast:	n/a	n/a
29	POLR2A	chr5:154208791-154209557	K562	blood:	n/a	n/a
30	FOSL1	chr5:154209114-154210109	HCT-116	colon:	n/a	n/a
31	POLR2A	chr5:154208874-154209594	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:154209115-154209939	HCT-116	colon:	n/a	n/a
33	FOS	chr5:154208763-154210508	MCF10A-Er-Src	breast:	n/a	n/a
34	SP1	chr5:154208774-154210165	HCT-116	colon:	n/a	n/a
35	RAD21	chr5:154208721-154209271	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:154206588..154209257-chr5:154235210..154237943,2	K562	blood:
2	chr5:154209195..154209843-chr5:154222467..154223169,2	MCF-7	breast:
3	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:
4	chr5:154207634..154212086-chr5:154212438..154216728,14	MCF-7	breast:
5	chr5:154209070..154210004-chr5:154224047..154224831,3	MCF-7	breast:
6	chr5:154133318..154137368-chr5:154208082..154212477,8	MCF-7	breast:
7	chr5:154200501..154205115-chr5:154206575..154209973,5	MCF-7	breast:

Variant related genes	Relation type
FAXDC2	TF binding region
ENSG00000155508	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11750475	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2461848	0.87[CEU][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs35879162	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56187116	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59199274	0.86[EUR][1000 genomes]
rs6580126	0.91[YRI][hapmap]

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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2560040	PRELP	trans	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
3	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
4	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
5	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
6	chr5:154193000-154211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:154194000-154209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:154195600-154214400	Weak transcription	Small Intestine	intestine
9	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
10	chr5:154196400-154214000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:154197600-154214400	Weak transcription	HUVEC	blood vessel
12	chr5:154197800-154214400	Weak transcription	Hela-S3	cervix
13	chr5:154198600-154211200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr5:154198600-154211400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:154199400-154214400	Weak transcription	Right Atrium	heart
16	chr5:154200200-154214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:154200800-154214000	Weak transcription	Fetal Heart	heart
18	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
19	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:154203600-154214400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:154203800-154210600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:154203800-154211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:154204000-154210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:154204200-154209600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:154204200-154211000	Weak transcription	Thymus	Thymus
26	chr5:154204200-154214400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:154204400-154210000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr5:154204400-154211400	Strong transcription	Liver	Liver
29	chr5:154204400-154213800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr5:154204400-154213800	Weak transcription	NHDF-Ad	bronchial
31	chr5:154204400-154214400	Weak transcription	Brain Germinal Matrix	brain
32	chr5:154205400-154211400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:154205800-154209800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:154205800-154211400	Strong transcription	Fetal Intestine Small	intestine
35	chr5:154206200-154209400	Enhancers	NHEK	skin
36	chr5:154206400-154212800	Strong transcription	Brain Anterior Caudate	brain
37	chr5:154206600-154210600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr5:154206600-154210800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:154206600-154211800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:154206800-154209400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:154206800-154210400	Enhancers	HMEC	breast
42	chr5:154206800-154211000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:154206800-154211000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr5:154206800-154211000	Strong transcription	Fetal Lung	lung
45	chr5:154206800-154211400	Genic enhancers	HepG2	liver
46	chr5:154207000-154211400	Strong transcription	Brain Substantia Nigra	brain
47	chr5:154207200-154209400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr5:154207200-154210000	Strong transcription	Placenta	Placenta
49	chr5:154207200-154210200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:154207200-154210800	Strong transcription	Brain Inferior Temporal Lobe	brain

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