Variant report

Variant	rs2304719
Chromosome Location	chr15:74235500-74235501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74217872-74240199	U87	brain:	n/a	n/a
2	POLR2A	chr15:74215819-74242527	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74235429..74237586-chr15:74282508..74284400,2	MCF-7	breast:
2	chr15:74231331..74232913-chr15:74233031..74235989,2	K562	blood:
3	chr15:74234935..74236699-chr15:74244847..74247930,3	K562	blood:
4	chr15:74234590..74236876-chr15:74248649..74250565,2	MCF-7	breast:
5	chr15:74233799..74236609-chr15:74239283..74241933,2	K562	blood:
6	chr15:74234337..74237104-chr15:74240874..74243639,2	MCF-7	breast:
7	chr15:74234935..74236699-chr15:74245732..74247930,2	K562	blood:

No data

Variant related genes	Relation type
LOXL1	TF binding region
ENSG00000129038	Chromatin interaction
ENSG00000067221	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2304720	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72745367	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74026308	0.93[AFR][1000 genomes]
rs8041642	1.00[ASW][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs9944214	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043335	chr15:74078689-74241186	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1603	chr15:74191222-74235733	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2304719	SENP8	cis	cerebellum	SCAN
rs2304719	RPP25	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74222600-74243200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:74227600-74236600	Weak transcription	Thymus	Thymus
3	chr15:74228400-74239600	Weak transcription	Pancreas	Pancrea
4	chr15:74228800-74243200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:74229000-74236600	Weak transcription	Brain Substantia Nigra	brain
6	chr15:74229000-74243000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:74229200-74236400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:74229200-74236800	Weak transcription	Esophagus	oesophagus
9	chr15:74229200-74241000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:74229600-74237000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:74230000-74236400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:74230000-74236600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:74230000-74239200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:74230200-74236400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:74231400-74235600	Enhancers	Aorta	Aorta
16	chr15:74231400-74238000	Enhancers	Placenta	Placenta
17	chr15:74231800-74242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:74232200-74235600	Enhancers	Spleen	Spleen
19	chr15:74232400-74236600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:74232600-74239400	Weak transcription	Brain Anterior Caudate	brain
21	chr15:74232600-74243000	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:74232800-74244000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:74233000-74236000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:74233000-74237200	Weak transcription	Fetal Kidney	kidney
25	chr15:74233000-74237600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:74233400-74240200	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:74233400-74243000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:74233600-74235600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr15:74233600-74243200	Weak transcription	Colonic Mucosa	Colon
30	chr15:74233800-74235800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:74233800-74236400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:74233800-74236800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:74233800-74237000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:74233800-74243800	Weak transcription	Stomach Mucosa	stomach
35	chr15:74234000-74237800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:74234000-74238000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:74234200-74240000	Enhancers	Fetal Thymus	thymus
38	chr15:74234400-74236600	Weak transcription	Left Ventricle	heart
39	chr15:74234400-74236600	Weak transcription	Ovary	ovary
40	chr15:74234400-74236800	Weak transcription	Lung	lung
41	chr15:74234600-74236600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:74234600-74236600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:74234600-74237400	Weak transcription	Fetal Brain Female	brain
44	chr15:74234600-74237600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:74234600-74243200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:74234800-74235600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:74234800-74236400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:74234800-74236400	Weak transcription	HMEC	breast
49	chr15:74234800-74236600	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:74234800-74236600	Weak transcription	Right Atrium	heart

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