Variant report

Variant	rs5753113
Chromosome Location	chr22:30780936-30780937
allele	G/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30780810..30782737-chr22:30819771..30822166,2	MCF-7	breast:
2	chr22:30713647..30715553-chr22:30779005..30781770,2	MCF-7	breast:
3	chr22:30682486..30684766-chr22:30780472..30782448,3	K562	blood:
4	chr22:30780386..30782265-chr22:30815840..30818586,2	MCF-7	breast:
5	chr22:30681125..30685749-chr22:30780011..30785695,7	MCF-7	breast:
6	chr22:30775755..30777572-chr22:30777818..30782197,3	K562	blood:
7	chr22:30683076..30686857-chr22:30780059..30784684,12	MCF-7	breast:
8	chr22:30768241..30771846-chr22:30779941..30783662,3	MCF-7	breast:
9	chr22:30660277..30662001-chr22:30780639..30782477,2	MCF-7	breast:
10	chr22:30779604..30781335-chr22:30790630..30793179,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242114	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000099985	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000187860	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1002189	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1076271	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076295	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1076297	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1076298	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1076299	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1079227	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11705092	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11912350	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11913885	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13053375	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13053595	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13054303	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13055431	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13056326	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13057340	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13057861	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17656850	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17657174	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17657653	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17657701	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17658238	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17730485	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17730538	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17736937	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1990268	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2229807	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2240420	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2299825	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28360656	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34367123	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34995457	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35293738	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35537171	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35711436	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35782599	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4390846	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4820005	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4820006	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4820007	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4820835	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4820836	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4820838	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820839	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4823089	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55979575	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56300819	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5749062	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5749063	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5749067	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5749075	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5749076	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5749077	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5749080	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5749081	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749086	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5749087	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5749088	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753058	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5753060	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753061	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753069	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753070	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753073	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753078	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5753082	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5753095	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5753096	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753097	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5753101	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753105	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753106	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753110	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753118	0.92[ASN][1000 genomes]
rs5753127	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763928	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5763932	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61322750	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62228968	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287175	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7287908	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7288947	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs737750	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs737751	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs737813	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs737948	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs740084	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740220	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs740222	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs740223	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs757868	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8136826	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer 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 target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5753113	RP1-130H16.16	cis	lung	GTEx
rs5753113	RP1-130H16.16	cis	Thyroid	GTEx
rs5753113	RP1-130H16.16	cis	Esophagus Muscularis	GTEx
rs5753113	RP1-130H16.16	cis	Artery Aorta	GTEx
rs5753113	RNF215	cis	Heart Left Ventricle	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30753200-30782200	Weak transcription	Stomach Mucosa	stomach
2	chr22:30753600-30782000	Weak transcription	Colonic Mucosa	Colon
3	chr22:30753600-30782000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr22:30753600-30782200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr22:30753600-30782400	Weak transcription	Primary T cells from cord blood	blood
6	chr22:30754200-30782000	Weak transcription	Fetal Brain Male	brain
7	chr22:30759600-30782200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr22:30762000-30782400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr22:30764000-30782200	Weak transcription	Right Atrium	heart
10	chr22:30766400-30782200	Weak transcription	Fetal Kidney	kidney
11	chr22:30768600-30781800	Strong transcription	Fetal Stomach	stomach
12	chr22:30769200-30782200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr22:30769200-30782200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:30770200-30781200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr22:30771200-30781000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:30772000-30783000	Weak transcription	Small Intestine	intestine
17	chr22:30772200-30782000	Weak transcription	NHDF-Ad	bronchial
18	chr22:30773800-30782200	Weak transcription	HMEC	breast
19	chr22:30774200-30782000	Weak transcription	A549	lung
20	chr22:30774200-30782200	Weak transcription	Brain Substantia Nigra	brain
21	chr22:30774200-30782400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr22:30774200-30782400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr22:30774400-30782400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr22:30775600-30782200	Weak transcription	Fetal Lung	lung
25	chr22:30775800-30782000	Weak transcription	Colon Smooth Muscle	Colon
26	chr22:30776000-30782000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:30776000-30782200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr22:30776200-30782200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr22:30776200-30782200	Weak transcription	GM12878-XiMat	blood
30	chr22:30776400-30782200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr22:30776600-30782400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr22:30776800-30782200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr22:30777000-30782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr22:30777400-30782000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr22:30777800-30782000	Weak transcription	Osteobl	bone
36	chr22:30777800-30782400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr22:30778000-30782200	Weak transcription	Esophagus	oesophagus
38	chr22:30778000-30782400	Weak transcription	Aorta	Aorta
39	chr22:30779200-30782200	Weak transcription	HUVEC	blood vessel
40	chr22:30779400-30782000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:30779400-30782400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr22:30779600-30782000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr22:30779600-30782200	Weak transcription	Right Ventricle	heart
44	chr22:30779600-30782400	Weak transcription	Left Ventricle	heart
45	chr22:30779800-30782200	Weak transcription	Gastric	stomach
46	chr22:30780000-30782200	Weak transcription	Fetal Heart	heart
47	chr22:30780200-30781800	Weak transcription	Fetal Thymus	thymus
48	chr22:30780200-30782000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr22:30780200-30782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:30780200-30782000	Weak transcription	Liver	Liver

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