Variant report

Variant	rs55701931
Chromosome Location	chr1:93555985-93555986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93544793..93547390-chr1:93553963..93556551,2	K562	blood:
2	chr1:93551871..93559721-chr1:93563340..93568184,9	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11164874	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164878	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11164882	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11586323	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12057476	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12064785	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12066315	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12067005	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12087466	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12088338	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12094547	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1414367	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17131699	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2391227	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2484485	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2749735	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2783492	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2783498	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2783506	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2815408	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2815409	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2815410	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2815411	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2815412	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2815414	0.81[EUR][1000 genomes]
rs36057148	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs505531	0.82[EUR][1000 genomes]
rs506556	0.81[EUR][1000 genomes]
rs546	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs667680	0.83[AFR][1000 genomes]
rs671559	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71510760	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs797660	0.83[AFR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv508404	chr1:93547383-93580012	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs55701931	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs55701931	RP4-717I23.3	cis	Whole Blood	GTEx
rs55701931	RP4-717I23.3	cis	Artery Aorta	GTEx
rs55701931	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs55701931	RP4-717I23.3	cis	lung	GTEx
rs55701931	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs55701931	RP4-717I23.3	cis	Stomach	GTEx
rs55701931	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs55701931	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs55701931	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs55701931	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs55701931	RP4-717I23.3	cis	Thyroid	GTEx
rs55701931	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs55701931	RP4-717I23.3	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93545800-93563200	Weak transcription	Esophagus	oesophagus
2	chr1:93545800-93568000	Weak transcription	Gastric	stomach
3	chr1:93545800-93578400	Weak transcription	Pancreas	Pancrea
4	chr1:93546000-93560600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:93546000-93573000	Weak transcription	Placenta	Placenta
6	chr1:93546200-93563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
8	chr1:93546400-93563200	Weak transcription	Psoas Muscle	Psoas
9	chr1:93546400-93567200	Weak transcription	Right Atrium	heart
10	chr1:93546400-93569400	Weak transcription	Ovary	ovary
11	chr1:93546600-93559000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:93546800-93556800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:93547200-93559000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:93547200-93576800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:93547600-93559400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:93547600-93559400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:93547600-93560200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:93547600-93580600	Weak transcription	Adipose Nuclei	Adipose
20	chr1:93547600-93580600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
22	chr1:93547800-93575400	Weak transcription	Hela-S3	cervix
23	chr1:93547800-93580600	Weak transcription	Fetal Kidney	kidney
24	chr1:93548000-93559000	Weak transcription	NHDF-Ad	bronchial
25	chr1:93548000-93601800	Weak transcription	NHLF	lung
26	chr1:93548200-93558200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:93548200-93576600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:93548200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:93548200-93576800	Weak transcription	Osteobl	bone
30	chr1:93548200-93578400	Weak transcription	Lung	lung
31	chr1:93548600-93569400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:93548800-93559000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:93548800-93559600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
35	chr1:93549000-93576800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:93549000-93582400	Weak transcription	HMEC	breast
37	chr1:93549000-93582800	Weak transcription	NHEK	skin
38	chr1:93550000-93556200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:93550000-93559400	Weak transcription	Brain Substantia Nigra	brain
40	chr1:93550600-93572600	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:93551400-93558600	Weak transcription	HepG2	liver
42	chr1:93551400-93563400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:93551400-93579800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:93551600-93556000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:93551600-93558400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:93551600-93559000	Weak transcription	Thymus	Thymus
47	chr1:93551600-93559200	Weak transcription	Liver	Liver
48	chr1:93551600-93559800	Weak transcription	Brain Anterior Caudate	brain
49	chr1:93551600-93570800	Weak transcription	HUVEC	blood vessel
50	chr1:93551600-93571000	Weak transcription	Fetal Intestine Large	intestine

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