Variant report

Variant	rs73402879
Chromosome Location	chr15:52429541-52429542
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	EP300	chr15:52429476-52429973	HepG2	liver:	n/a	n/a
2	HNF4G	chr15:52429486-52430109	HepG2	liver:	n/a	chr15:52429768-52429781 chr15:52429766-52429781 chr15:52429769-52429782 chr15:52429768-52429782 chr15:52429769-52429781 chr15:52429768-52429782 chr15:52429769-52429781 chr15:52429770-52429782 chr15:52429766-52429784 chr15:52429769-52429781 chr15:52429768-52429783 chr15:52429768-52429782
3	HNF4G	chr15:52429505-52429975	HepG2	liver:	n/a	chr15:52429768-52429781 chr15:52429766-52429781 chr15:52429769-52429782 chr15:52429768-52429782 chr15:52429769-52429781 chr15:52429768-52429782 chr15:52429769-52429781 chr15:52429770-52429782 chr15:52429766-52429784 chr15:52429769-52429781 chr15:52429768-52429783 chr15:52429768-52429782
4	HNF4A	chr15:52429500-52430024	HepG2	liver:	n/a	chr15:52429768-52429781 chr15:52429769-52429782 chr15:52429768-52429782 chr15:52429769-52429781 chr15:52429768-52429782 chr15:52429767-52429782 chr15:52429769-52429781 chr15:52429770-52429782 chr15:52429766-52429784 chr15:52429769-52429781 chr15:52429768-52429783 chr15:52429768-52429782
5	SP1	chr15:52429515-52430031	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52309759..52313480-chr15:52429073..52432426,3	K562	blood:
2	chr15:52263277..52265007-chr15:52427883..52430038,2	MCF-7	breast:
3	chr15:52418771..52421599-chr15:52429472..52431548,2	MCF-7	breast:
4	chr15:52309643..52312109-chr15:52424380..52429568,4	MCF-7	breast:
5	chr15:52310998..52312915-chr15:52428801..52431088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259709	TF binding region
GNB5	TF binding region
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs16953085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7163133	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402857	0.93[AFR][1000 genomes]
rs73402859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402869	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035146	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv2571437	chr15:52429466-52430919	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52412200-52436000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:52413600-52431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:52416000-52432800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:52416200-52431600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:52417000-52436000	Weak transcription	Lung	lung
11	chr15:52417200-52431200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:52417200-52431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:52417200-52436200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:52417400-52431800	Weak transcription	HMEC	breast
15	chr15:52417400-52432000	Weak transcription	NHDF-Ad	bronchial
16	chr15:52417600-52435400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:52417800-52431800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:52420400-52433600	Strong transcription	Ovary	ovary
19	chr15:52421800-52431800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:52422600-52431200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52423000-52436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:52423000-52458200	Weak transcription	Dnd41	blood
24	chr15:52423600-52431800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:52424000-52441200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:52424200-52430400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:52424600-52432400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:52425000-52430000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:52425000-52430400	Enhancers	Pancreas	Pancrea
30	chr15:52425200-52429600	Enhancers	HepG2	liver
31	chr15:52425600-52432400	Enhancers	Liver	Liver
32	chr15:52425800-52430000	Enhancers	Small Intestine	intestine
33	chr15:52425800-52432600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:52425800-52435400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:52426000-52430200	Enhancers	Fetal Intestine Small	intestine
36	chr15:52426600-52430000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr15:52426800-52430200	Enhancers	Colonic Mucosa	Colon
38	chr15:52426800-52430200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr15:52426800-52430400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:52426800-52432200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:52427200-52430400	Enhancers	Placenta	Placenta
42	chr15:52427400-52430200	Enhancers	Fetal Thymus	thymus
43	chr15:52427400-52430200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr15:52427400-52430400	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr15:52427400-52430400	Strong transcription	NHEK	skin
46	chr15:52427400-52432200	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:52427400-52432200	Weak transcription	Brain Angular Gyrus	brain
48	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
49	chr15:52427600-52429600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:52427600-52429600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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