Variant report

Variant	rs11164874
Chromosome Location	chr1:93580402-93580403
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93579998..93581880-chr1:93596682..93599849,3	K562	blood:
2	chr1:93567850..93570397-chr1:93578761..93580603,2	K562	blood:
3	chr1:93561194..93562759-chr1:93579663..93581219,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11164878	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164882	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11586323	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12057476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12066315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12067005	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12087466	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088338	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12094547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1414367	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17131699	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2391227	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2484485	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2749735	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2783492	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2783498	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2783506	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815408	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2815409	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2815410	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815411	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815412	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2815413	0.82[EUR][1000 genomes]
rs2815414	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36057148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505531	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs506556	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs522999	0.82[EUR][1000 genomes]
rs546	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55701931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs581825	0.81[EUR][1000 genomes]
rs615416	0.82[EUR][1000 genomes]
rs658877	0.82[EUR][1000 genomes]
rs667680	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs671559	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71510760	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs797660	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[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	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	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11164874	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs11164874	RP4-717I23.3	cis	lung	GTEx
rs11164874	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs11164874	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs11164874	RP4-717I23.3	cis	Artery Aorta	GTEx
rs11164874	RP4-717I23.3	cis	Stomach	GTEx
rs11164874	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs11164874	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11164874	RP4-717I23.3	cis	Artery Tibial	GTEx
rs11164874	RP4-717I23.3	cis	Whole Blood	GTEx
rs11164874	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs11164874	RP4-717I23.3	cis	Thyroid	GTEx
rs11164874	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs11164874	RP4-717I23.3	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:93547600-93580600	Weak transcription	Adipose Nuclei	Adipose
4	chr1:93547600-93580600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
6	chr1:93547800-93580600	Weak transcription	Fetal Kidney	kidney
7	chr1:93548000-93601800	Weak transcription	NHLF	lung
8	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
9	chr1:93549000-93582400	Weak transcription	HMEC	breast
10	chr1:93549000-93582800	Weak transcription	NHEK	skin
11	chr1:93555400-93581000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:93559400-93581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:93560200-93581600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:93563400-93582000	Weak transcription	Esophagus	oesophagus
15	chr1:93564000-93581800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
17	chr1:93568400-93584200	Weak transcription	Fetal Brain Male	brain
18	chr1:93570000-93582200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:93570200-93581600	Weak transcription	Ovary	ovary
20	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
21	chr1:93571600-93581600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
23	chr1:93573000-93580600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:93573600-93580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:93573600-93581000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:93573600-93586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:93573800-93582000	Weak transcription	Brain Germinal Matrix	brain
29	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
30	chr1:93574200-93581200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:93574200-93581600	Weak transcription	Fetal Brain Female	brain
32	chr1:93574200-93582600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:93574600-93581000	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:93574600-93584800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:93574600-93585800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:93574600-93609000	Strong transcription	Dnd41	blood
38	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
39	chr1:93575000-93581000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:93575200-93589800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:93575400-93581000	Weak transcription	Gastric	stomach
42	chr1:93575800-93589200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:93576000-93580600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:93576000-93581000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:93576000-93581600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:93576200-93581600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:93576400-93582000	Weak transcription	Hela-S3	cervix
48	chr1:93577000-93580600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:93577200-93580600	Weak transcription	A549	lung
50	chr1:93577200-93592800	Weak transcription	Colon Smooth Muscle	Colon

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