Variant report

Variant	rs2304722
Chromosome Location	chr15:74241749-74241750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74238556..74240155-chr15:74240759..74243694,2	MCF-7	breast:
2	chr15:74234337..74237104-chr15:74240874..74243639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129038	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1992314	0.82[YRI][hapmap]
rs2028387	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs28758267	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886776	0.90[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs58270968	0.85[AFR][1000 genomes]
rs66473812	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66481504	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66497556	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67182653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72745365	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72745372	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs893816	0.82[ASW][hapmap];0.95[LWK][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs893818	0.82[YRI][hapmap]
rs893821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2304722	LOXL1	cis	parietal	SCAN

Chromatin state (count:79 , 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	chr15:74228800-74243200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:74229000-74243000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:74231800-74242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:74232600-74243000	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:74232800-74244000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:74233400-74243000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:74233600-74243200	Weak transcription	Colonic Mucosa	Colon
9	chr15:74233800-74243800	Weak transcription	Stomach Mucosa	stomach
10	chr15:74234600-74243200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:74234800-74249400	Weak transcription	Primary T cells from cord blood	blood
12	chr15:74235200-74243400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:74235400-74243400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:74236400-74243000	Weak transcription	Brain Germinal Matrix	brain
15	chr15:74236800-74241800	Strong transcription	Osteobl	bone
16	chr15:74237000-74242400	Strong transcription	NH-A	brain
17	chr15:74237000-74242600	Strong transcription	NHLF	lung
18	chr15:74237000-74242800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:74237000-74242800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr15:74237000-74243200	Weak transcription	Right Atrium	heart
21	chr15:74237000-74243400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:74237000-74243800	Weak transcription	Fetal Intestine Large	intestine
23	chr15:74237200-74242200	Strong transcription	NHDF-Ad	bronchial
24	chr15:74237200-74242800	Weak transcription	Esophagus	oesophagus
25	chr15:74237200-74243400	Weak transcription	Brain Substantia Nigra	brain
26	chr15:74237200-74247800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:74237400-74242200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:74237400-74242800	Strong transcription	Fetal Lung	lung
29	chr15:74237600-74241800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:74237600-74242400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:74237600-74242400	Weak transcription	Fetal Brain Male	brain
32	chr15:74237600-74242800	Weak transcription	Fetal Brain Female	brain
33	chr15:74237600-74243000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:74237600-74243000	Weak transcription	Brain Angular Gyrus	brain
35	chr15:74237600-74243200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:74237600-74243200	Weak transcription	Primary B cells from cord blood	blood
37	chr15:74237800-74242000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:74237800-74242600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:74237800-74242800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:74237800-74243000	Weak transcription	Spleen	Spleen
41	chr15:74237800-74243400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:74238000-74243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:74238000-74243000	Strong transcription	Fetal Stomach	stomach
44	chr15:74238000-74243800	Weak transcription	Fetal Kidney	kidney
45	chr15:74238400-74242200	Strong transcription	Placenta	Placenta
46	chr15:74238600-74243000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr15:74238800-74242200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:74238800-74242200	Strong transcription	Gastric	stomach
49	chr15:74238800-74242400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:74238800-74242400	Strong transcription	Aorta	Aorta

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