Variant report

Variant	rs629550
Chromosome Location	chr18:11947184-11947185
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	chr18:11943655..11945361-chr18:11945655..11947239,2	K562	blood:
2	chr18:11942200..11944403-chr18:11945957..11947615,2	K562	blood:
3	chr18:11945871..11949775-chr18:11972448..11976477,3	K562	blood:
4	chr18:11944456..11952400-chr18:11978684..11982486,15	K562	blood:
5	chr18:11938000..11939656-chr18:11946087..11948724,2	K562	blood:
6	chr18:11943801..11947480-chr18:11981525..11984599,3	MCF-7	breast:
7	chr18:11945775..11953098-chr18:11977697..11982837,16	K562	blood:
8	chr18:11927997..11930119-chr18:11947025..11949213,2	K562	blood:
9	chr18:11946068..11950381-chr18:11979395..11982010,5	MCF-7	breast:
10	chr18:11947089..11947879-chr19:797034..797866,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000011304	Chromatin interaction
ENSG00000267661	Chromatin interaction
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1811452	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478333	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34803006	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35932750	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591880	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604427	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604453	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622863	0.95[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648676	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs649039	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649459	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662981	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677254	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs677359	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679158	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694635	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226885	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7227036	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9952563	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9962395	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	nsv1063339	chr18:11909588-11979264	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv576495	chr18:11917410-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription 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
9	nsv909385	chr18:11938102-11986557	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs629550	RP11-820I16.1	cis	Thyroid	GTEx
rs629550	RP11-820I16.1	cis	Artery Tibial	GTEx
rs629550	RP11-820I16.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11939000-11947200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:11941600-11947400	Enhancers	Placenta	Placenta
3	chr18:11943800-11947600	Weak transcription	Gastric	stomach
4	chr18:11945800-11947200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr18:11945800-11947200	Enhancers	Colonic Mucosa	Colon
6	chr18:11946000-11947200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr18:11946000-11947200	Enhancers	Esophagus	oesophagus
8	chr18:11946000-11947200	Enhancers	Left Ventricle	heart
9	chr18:11946000-11947200	Flanking Active TSS	Hela-S3	cervix
10	chr18:11946000-11947400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:11946000-11947400	Enhancers	Pancreas	Pancrea
12	chr18:11946000-11947800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:11946200-11947200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr18:11946200-11947200	Enhancers	Fetal Intestine Large	intestine
15	chr18:11946200-11947200	Enhancers	Fetal Muscle Trunk	muscle
16	chr18:11946200-11947400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr18:11946200-11947400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr18:11946200-11947400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr18:11946200-11947400	Weak transcription	Lung	lung
20	chr18:11946200-11947600	Enhancers	Stomach Mucosa	stomach
21	chr18:11946200-11948400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr18:11946400-11947200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr18:11946600-11947200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr18:11946600-11947200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr18:11946600-11947200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr18:11946600-11947200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:11946600-11947200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr18:11946600-11947200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr18:11946600-11947200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr18:11946600-11947200	Enhancers	Brain Cingulate Gyrus	brain
31	chr18:11946600-11947200	Enhancers	Fetal Heart	heart
32	chr18:11946600-11947200	Enhancers	Fetal Kidney	kidney
33	chr18:11946600-11947200	Flanking Active TSS	K562	blood
34	chr18:11946600-11947200	Flanking Active TSS	NHEK	skin
35	chr18:11946600-11947400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr18:11946600-11948000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr18:11946600-11948000	Enhancers	HMEC	breast
38	chr18:11946600-11948200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:11946600-11948200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr18:11946600-11948200	Flanking Active TSS	Osteobl	bone
41	chr18:11946600-11948400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr18:11946800-11947200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr18:11946800-11947200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:11946800-11947200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr18:11946800-11947200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr18:11946800-11947200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr18:11946800-11947200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr18:11946800-11947200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr18:11946800-11947200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr18:11946800-11947200	Flanking Active TSS	Brain Anterior Caudate	brain

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