Variant report

Variant	rs58115308
Chromosome Location	chr17:18178984-18178985
allele	C/T
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	chr17:18178901-18179109	K562	blood:	n/a	n/a
2	CEBPB	chr17:18178971-18179028	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:18178636-18179002	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18164305..18167744-chr17:18176383..18179397,3	K562	blood:
2	chr17:18178546..18181267-chr17:18181551..18184917,3	MCF-7	breast:

Variant related genes	Relation type
TOP3A	TF binding region
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs17855350	1.00[EUR][1000 genomes]
rs28694704	1.00[EUR][1000 genomes]
rs56109231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56180580	1.00[EUR][1000 genomes]
rs56735648	1.00[EUR][1000 genomes]
rs56793258	1.00[EUR][1000 genomes]
rs58499955	1.00[EUR][1000 genomes]
rs59738176	1.00[EUR][1000 genomes]
rs59867698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60320587	1.00[EUR][1000 genomes]
rs60510653	1.00[EUR][1000 genomes]
rs60699593	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60708953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60814048	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61361031	1.00[EUR][1000 genomes]
rs61576260	1.00[EUR][1000 genomes]
rs7207131	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207489	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7213472	1.00[EUR][1000 genomes]
rs7213789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7219191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7226015	1.00[EUR][1000 genomes]
rs73288279	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288297	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288302	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73289913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73980805	1.00[EUR][1000 genomes]
rs8064901	1.00[EUR][1000 genomes]
rs8068530	1.00[EUR][1000 genomes]
rs8069012	1.00[EUR][1000 genomes]
rs8071028	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071911	1.00[EUR][1000 genomes]
rs8074322	1.00[EUR][1000 genomes]
rs8080816	1.00[EUR][1000 genomes]
rs8082574	1.00[AMR][1000 genomes]
rs9910599	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
2	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
5	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
7	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
8	chr17:18168800-18179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:18168800-18179400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:18169000-18181200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr17:18169200-18179400	Weak transcription	NHDF-Ad	bronchial
13	chr17:18171000-18183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr17:18172400-18201000	Strong transcription	Fetal Stomach	stomach
16	chr17:18172600-18181800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:18172800-18198400	Strong transcription	Thymus	Thymus
18	chr17:18173000-18198400	Strong transcription	Fetal Thymus	thymus
19	chr17:18173000-18199000	Strong transcription	Primary T cells from cord blood	blood
20	chr17:18173000-18200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:18173200-18198400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr17:18173200-18200200	Strong transcription	Placenta	Placenta
24	chr17:18173400-18183600	Weak transcription	Fetal Heart	heart
25	chr17:18173400-18198200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr17:18173400-18198400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr17:18173400-18198800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:18173400-18200200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:18173400-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:18173400-18201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:18173400-18201000	Strong transcription	Fetal Intestine Small	intestine
32	chr17:18173600-18190800	Strong transcription	A549	lung
33	chr17:18173600-18198200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr17:18173600-18200200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:18173600-18200800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr17:18174000-18200600	Strong transcription	Dnd41	blood
37	chr17:18174200-18200600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr17:18174600-18181000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:18174800-18182400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:18174800-18190600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr17:18174800-18198600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:18174800-18200600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr17:18175400-18189400	Strong transcription	NHLF	lung
44	chr17:18175600-18181800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr17:18175600-18189200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:18175600-18196600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:18175600-18200800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr17:18175800-18180200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr17:18175800-18181800	Strong transcription	GM12878-XiMat	blood
50	chr17:18175800-18184000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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