Variant report

Variant	rs56153053
Chromosome Location	chr17:17824757-17824758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17822649..17827287-chr17:17828107..17833962,6	MCF-7	breast:
2	chr17:17822751..17824989-chr17:17833618..17835263,2	K562	blood:
3	chr17:17822590..17824819-chr17:17873819..17875966,2	MCF-7	breast:
4	chr17:17578891..17581684-chr17:17824075..17825729,2	K562	blood:
5	chr17:17815608..17820314-chr17:17821294..17824866,4	MCF-7	breast:
6	chr17:17722826..17725491-chr17:17823665..17826462,2	K562	blood:
7	chr17:17822871..17825553-chr17:17834729..17836696,2	MCF-7	breast:
8	chr17:17823331..17826317-chr17:17843856..17846226,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223979	Chromatin interaction
ENSG00000175662	Chromatin interaction
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs16960767	1.00[AMR][1000 genomes]
rs16960818	1.00[AMR][1000 genomes]
rs56054716	1.00[AMR][1000 genomes]
rs56160247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56232485	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56928492	1.00[AMR][1000 genomes]
rs57082481	1.00[AMR][1000 genomes]
rs57134764	1.00[EUR][1000 genomes]
rs57277459	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57791826	1.00[AMR][1000 genomes]
rs58116638	1.00[EUR][1000 genomes]
rs58219643	1.00[AMR][1000 genomes]
rs58376085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58676524	1.00[AMR][1000 genomes]
rs58936409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58970292	1.00[EUR][1000 genomes]
rs61050785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61060916	1.00[AMR][1000 genomes]
rs61188141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61256737	1.00[AMR][1000 genomes]
rs7218054	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7218246	1.00[AMR][1000 genomes]
rs7218594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221934	1.00[AMR][1000 genomes]
rs7224621	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297834	1.00[AMR][1000 genomes]
rs73297855	1.00[AMR][1000 genomes]
rs73297868	1.00[AMR][1000 genomes]
rs73299861	1.00[AMR][1000 genomes]
rs73299873	1.00[AMR][1000 genomes]
rs73299892	1.00[AMR][1000 genomes]
rs73301827	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73301859	1.00[AMR][1000 genomes]
rs73301894	1.00[AMR][1000 genomes]
rs73303812	1.00[AMR][1000 genomes]
rs73303813	1.00[AMR][1000 genomes]
rs73303833	1.00[AMR][1000 genomes]
rs73303840	1.00[EUR][1000 genomes]
rs73303844	1.00[EUR][1000 genomes]
rs73303854	1.00[AMR][1000 genomes]
rs73303856	1.00[AMR][1000 genomes]
rs73303857	1.00[AMR][1000 genomes]
rs73305952	1.00[AMR][1000 genomes]
rs73979211	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73979243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73981076	1.00[AMR][1000 genomes]
rs8066528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066865	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8067146	1.00[EUR][1000 genomes]
rs8068860	1.00[EUR][1000 genomes]
rs8078368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9914362	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	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
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17810800-17838400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:17811400-17838400	Weak transcription	Primary T cells from cord blood	blood
3	chr17:17814800-17833200	Weak transcription	Aorta	Aorta
4	chr17:17817600-17831600	Weak transcription	Fetal Brain Female	brain
5	chr17:17817800-17838200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr17:17820800-17826400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:17821000-17828400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:17821200-17829000	Enhancers	NHEK	skin
9	chr17:17821600-17824800	Weak transcription	Pancreas	Pancrea
10	chr17:17821600-17827200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:17821800-17826400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr17:17821800-17827200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:17821800-17827200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:17821800-17828400	Enhancers	HMEC	breast
15	chr17:17822000-17824800	Enhancers	HSMMtube	muscle
16	chr17:17822000-17826600	Enhancers	NHDF-Ad	bronchial
17	chr17:17822000-17827000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:17822000-17827200	Enhancers	Brain Hippocampus Middle	brain
19	chr17:17822000-17836600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:17822200-17826400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:17822200-17826600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:17822200-17826600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr17:17822200-17827000	Enhancers	Brain Substantia Nigra	brain
24	chr17:17822400-17824800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:17822400-17828400	Enhancers	NH-A	brain
26	chr17:17822600-17826800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:17823000-17824800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr17:17823000-17825400	Weak transcription	Fetal Brain Male	brain
29	chr17:17823200-17838000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:17823200-17838200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:17823400-17824800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:17823400-17824800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:17823400-17824800	Weak transcription	Colonic Mucosa	Colon
34	chr17:17823400-17825000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:17823400-17825600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr17:17823400-17828200	Weak transcription	GM12878-XiMat	blood
37	chr17:17823400-17836400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:17823400-17838200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:17823600-17827800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr17:17823800-17826600	Enhancers	Brain Anterior Caudate	brain
41	chr17:17823800-17826600	Enhancers	Fetal Muscle Leg	muscle
42	chr17:17824000-17824800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:17824000-17824800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr17:17824000-17825200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:17824000-17825200	Enhancers	Fetal Heart	heart
46	chr17:17824000-17825600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr17:17824000-17826400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr17:17824000-17826400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:17824000-17826400	Enhancers	Duodenum Mucosa	Duodenum
50	chr17:17824000-17826600	Enhancers	Placenta Amnion	Placenta Amnion

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