Variant report

Variant	rs61648928
Chromosome Location	chr15:39721821-39721822
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	chr15:39721760-39723490	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: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10459586	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10520130	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070198	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070206	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070207	0.85[ASN][1000 genomes]
rs1158915	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158916	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158917	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854059	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854786	0.81[EUR][1000 genomes]
rs11855535	0.81[EUR][1000 genomes]
rs11855543	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855977	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855990	0.85[ASN][1000 genomes]
rs11857970	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148631	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1551945	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16952151	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969038	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16969104	0.88[ASN][1000 genomes]
rs3889532	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4286083	0.88[ASN][1000 genomes]
rs4923830	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924362	0.88[ASN][1000 genomes]
rs5028679	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56839831	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56869025	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57248361	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58417285	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171584	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73393497	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008128	0.81[AMR][1000 genomes]
rs8025111	0.88[ASN][1000 genomes]
rs8032303	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8034569	0.86[EUR][1000 genomes];0.88[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

No data

Chromatin state (count:65 , 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	chr15:39719600-39722000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:39719600-39723400	Enhancers	Fetal Thymus	thymus
9	chr15:39719600-39724200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:39719600-39725000	Weak transcription	Right Ventricle	heart
11	chr15:39719600-39727200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:39719800-39722400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:39719800-39725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:39720000-39722000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:39720000-39722000	Weak transcription	HSMMtube	muscle
16	chr15:39720000-39722200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:39720000-39722200	Weak transcription	Right Atrium	heart
18	chr15:39720000-39723800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:39720000-39724200	Enhancers	Thymus	Thymus
20	chr15:39720200-39722000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:39720200-39722000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:39720200-39722000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:39720200-39722000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:39720200-39722000	Weak transcription	HSMM	muscle
25	chr15:39720200-39722200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:39720200-39722200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:39720200-39722200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:39720200-39722200	Weak transcription	NHDF-Ad	bronchial
29	chr15:39720200-39723200	Enhancers	Primary T cells from cord blood	blood
30	chr15:39720200-39723800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:39720200-39723800	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:39720200-39723800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr15:39720200-39724000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:39720200-39725000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:39720200-39725000	Weak transcription	Fetal Stomach	stomach
36	chr15:39720200-39725600	Weak transcription	Lung	lung
37	chr15:39720200-39726800	Weak transcription	Adipose Nuclei	Adipose
38	chr15:39720400-39722000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:39720400-39722000	Weak transcription	NHLF	lung
40	chr15:39720400-39722200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:39720400-39722400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:39720400-39724000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:39720400-39726400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr15:39720600-39722000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:39720600-39722200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr15:39720800-39722600	Enhancers	Small Intestine	intestine
47	chr15:39721000-39722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:39721000-39722400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:39721000-39724200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:39721200-39722000	Weak transcription	HepG2	liver

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