Variant report

Variant	rs2445765
Chromosome Location	chr15:51634898-51634899
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	CTCF	chr15:51634800-51634950	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:51631962..51635284-chr15:51658030..51661576,5	MCF-7	breast:
2	chr15:51634192..51635133-chr15:51673006..51674097,3	MCF-7	breast:
3	chr15:51633614..51635996-chr15:51658332..51660020,2	MCF-7	breast:
4	chr15:51632518..51637077-chr15:51639957..51644018,8	MCF-7	breast:

Variant related genes	Relation type
CYP19A1	TF binding region
ENSG00000259194	Chromatin interaction
ENSG00000270378	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1071955	0.86[ASN][1000 genomes]
rs11070843	0.89[ASW][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11070844	0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs11070845	0.86[ASN][1000 genomes]
rs11630919	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11631118	1.00[ASW][hapmap];0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11632569	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11632571	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12101686	0.85[ASN][1000 genomes]
rs12440754	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12441382	0.89[ASW][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs12441859	0.89[ASW][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12592797	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12595133	0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12595379	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1458928	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1551656	0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs1870049	0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs1961177	0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs2124872	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2445766	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2445767	0.97[EUR][1000 genomes]
rs2445768	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2445773	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2445774	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2446405	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2446417	0.95[EUR][1000 genomes]
rs2446423	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2470163	0.95[EUR][1000 genomes]
rs28500524	0.86[ASN][1000 genomes]
rs6493495	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs6493497	0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs7167696	0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs7175922	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs7176005	0.86[ASN][1000 genomes]
rs7178417	0.85[AFR][1000 genomes]
rs8027683	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8031112	0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs8031184	0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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 miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2445765	GLDN	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51633400-51635000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr15:51633400-51635000	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr15:51633600-51635000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr15:51633600-51635200	Active TSS	Brain Angular Gyrus	brain
5	chr15:51633600-51635200	Active TSS	Brain Hippocampus Middle	brain
6	chr15:51633600-51635200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:51633600-51635200	Active TSS	Brain Substantia Nigra	brain
8	chr15:51633600-51635800	Active TSS	Brain Cingulate Gyrus	brain
9	chr15:51633800-51635000	Active TSS	Brain Anterior Caudate	brain
10	chr15:51634400-51635000	Enhancers	Spleen	Spleen
11	chr15:51634400-51635200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr15:51634600-51635000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr15:51634600-51635000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:51634600-51635000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:51634600-51635000	Bivalent Enhancer	Fetal Brain Male	brain
16	chr15:51634600-51635000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
17	chr15:51634600-51635200	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr15:51634600-51635800	Weak transcription	Aorta	Aorta
19	chr15:51634600-51636000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:51634800-51635000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:51634800-51635000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr15:51634800-51635000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:51634800-51635000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:51634800-51635000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:51634800-51635000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:51634800-51635000	Bivalent/Poised TSS	Osteobl	bone
27	chr15:51634800-51635200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:51634800-51635200	Flanking Active TSS	Placenta	Placenta
29	chr15:51634800-51641400	Weak transcription	Right Ventricle	heart
30	chr15:51634800-51643400	Weak transcription	Lung	lung

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