Variant report

Variant	rs28739021
Chromosome Location	chr15:59412034-59412035
allele	A/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	POLR2A	chr15:59411939-59412641	A549	lung:	n/a	n/a
2	POLR2A	chr15:59411906-59412106	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:59397489..59399180-chr15:59409328..59412119,2	K562	blood:
2	chr15:59409432..59412721-chr15:59414521..59417919,6	K562	blood:
3	chr15:59410488..59412721-chr15:59415903..59417708,3	K562	blood:

Variant related genes	Relation type
ENSG00000259732	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518998	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574500	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574501	0.89[EUR][1000 genomes]
rs13498	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940958	1.00[AMR][1000 genomes]
rs16940976	1.00[AMR][1000 genomes]
rs16941012	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16941048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941077	0.94[EUR][1000 genomes]
rs28383495	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28739025	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57164516	0.94[EUR][1000 genomes]
rs6494052	1.00[AMR][1000 genomes]
rs6494058	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6494067	0.93[AMR][1000 genomes]
rs7164061	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7171252	0.85[AMR][1000 genomes]
rs7173787	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173999	1.00[EUR][1000 genomes]
rs7174992	0.89[EUR][1000 genomes]
rs7175697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7177112	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7180666	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7181728	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74017367	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8026039	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8027376	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030514	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8030811	1.00[AMR][1000 genomes]
rs8032299	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8035952	1.00[AMR][1000 genomes]
rs8040605	0.86[AMR][1000 genomes]
rs8041633	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042601	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59397800-59415600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:59397800-59450000	Weak transcription	Small Intestine	intestine
3	chr15:59398000-59412200	Weak transcription	Spleen	Spleen
4	chr15:59398000-59423200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:59398000-59423400	Weak transcription	Esophagus	oesophagus
6	chr15:59398000-59425600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:59398000-59426000	Weak transcription	Lung	lung
8	chr15:59398000-59426200	Weak transcription	HSMMtube	muscle
9	chr15:59398000-59426400	Weak transcription	Left Ventricle	heart
10	chr15:59398000-59427200	Weak transcription	Pancreas	Pancrea
11	chr15:59398000-59427400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:59398000-59462000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:59398200-59415200	Weak transcription	Colonic Mucosa	Colon
14	chr15:59398200-59423800	Weak transcription	Fetal Brain Male	brain
15	chr15:59398600-59422600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:59399200-59417600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:59399200-59419600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:59399200-59420200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:59399200-59421600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:59399400-59413800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:59399400-59417400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:59399400-59418800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:59399400-59419600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:59399600-59413200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:59399600-59413400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:59399600-59413400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:59399600-59419600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:59399600-59437000	Strong transcription	Fetal Thymus	thymus
29	chr15:59399800-59413800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:59400000-59413200	Strong transcription	Fetal Stomach	stomach
31	chr15:59400600-59413600	Strong transcription	Hela-S3	cervix
32	chr15:59401000-59423200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:59401200-59439800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr15:59402000-59413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:59402200-59412600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:59402600-59412800	Strong transcription	NHLF	lung
37	chr15:59402600-59413400	Strong transcription	HMEC	breast
38	chr15:59402600-59413600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:59403600-59418200	Strong transcription	Dnd41	blood
40	chr15:59403800-59413000	Weak transcription	Fetal Heart	heart
41	chr15:59405000-59413800	Strong transcription	HepG2	liver
42	chr15:59405400-59419800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:59405600-59412600	Strong transcription	Osteobl	bone
44	chr15:59405600-59413400	Strong transcription	HSMM	muscle
45	chr15:59405600-59418800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:59405800-59413400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:59405800-59418000	Strong transcription	GM12878-XiMat	blood
48	chr15:59405800-59426000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:59406000-59412600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:59406000-59413600	Strong transcription	H1 Cell Line	embryonic stem cell

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