Variant report

Variant	rs4923826
Chromosome Location	chr15:39723045-39723046
allele	A/C
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	chr15:39721938-39723507	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:39722190-39723527	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr15:39721760-39723490	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:39722122-39723348	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr15:39721832-39723682	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39721051..39725636-chr15:39870055..39875310,7	MCF-7	breast:
2	chr15:39721562..39724453-chr15:39734811..39737253,2	MCF-7	breast:
3	chr15:39720867..39723371-chr15:39870394..39874925,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259345	TF binding region
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070202	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148895	0.81[EUR][1000 genomes]
rs12906753	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907239	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16969088	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4244569	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4306475	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4344715	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405525	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4417529	0.80[ASN][1000 genomes]
rs4522393	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924354	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55638424	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57817952	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58084121	0.88[EUR][1000 genomes]
rs59238363	0.88[EUR][1000 genomes]
rs6492889	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724098	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8026812	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8029673	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8032895	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4923826	RP11-624L4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39712600-39724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:39713200-39727400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:39719200-39723200	Enhancers	Left Ventricle	heart
4	chr15:39719200-39728200	Enhancers	HUVEC	blood vessel
5	chr15:39719400-39723400	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:39719400-39726800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:39719600-39723400	Enhancers	Fetal Thymus	thymus
8	chr15:39719600-39724200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:39719600-39725000	Weak transcription	Right Ventricle	heart
10	chr15:39719600-39727200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:39719800-39725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:39720000-39723800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr15:39720000-39724200	Enhancers	Thymus	Thymus
14	chr15:39720200-39723200	Enhancers	Primary T cells from cord blood	blood
15	chr15:39720200-39723800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:39720200-39723800	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:39720200-39723800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr15:39720200-39724000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:39720200-39725000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:39720200-39725000	Weak transcription	Fetal Stomach	stomach
21	chr15:39720200-39725600	Weak transcription	Lung	lung
22	chr15:39720200-39726800	Weak transcription	Adipose Nuclei	Adipose
23	chr15:39720400-39724000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:39720400-39726400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:39721000-39724200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:39721400-39723200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:39721400-39724000	Enhancers	NH-A	brain
28	chr15:39721600-39724400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:39721600-39724600	Enhancers	Osteobl	bone
30	chr15:39721800-39724400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:39721800-39725400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:39722000-39723200	Enhancers	Fetal Muscle Leg	muscle
33	chr15:39722000-39723200	Enhancers	HMEC	breast
34	chr15:39722000-39723200	Enhancers	HSMMtube	muscle
35	chr15:39722000-39723600	Enhancers	Fetal Lung	lung
36	chr15:39722000-39724000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:39722200-39723200	Enhancers	Right Atrium	heart
38	chr15:39722400-39727800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:39722600-39723200	Enhancers	NHEK	skin
40	chr15:39722600-39724200	Weak transcription	Fetal Heart	heart
41	chr15:39722600-39725000	Weak transcription	NHDF-Ad	bronchial
42	chr15:39722600-39725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:39722600-39725600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:39722600-39726800	Weak transcription	Small Intestine	intestine
45	chr15:39722600-39727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:39722800-39724000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:39722800-39724000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:39722800-39724200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:39722800-39724200	Weak transcription	Spleen	Spleen
50	chr15:39722800-39725600	Weak transcription	Duodenum Mucosa	Duodenum

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