Variant report

Variant	rs4471742
Chromosome Location	chr17:17877771-17877772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17874682..17878997-chr17:17883276..17886236,4	MCF-7	breast:
2	chr17:17741798..17744569-chr17:17877349..17878945,2	K562	blood:
3	chr17:17727418..17729272-chr17:17876604..17878211,2	K562	blood:

Variant related genes	Relation type
ENSG00000230273	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10048206	0.84[EUR][1000 genomes]
rs11078404	0.82[EUR][1000 genomes]
rs11078405	0.81[EUR][1000 genomes]
rs11078406	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11078407	0.83[EUR][1000 genomes]
rs11078408	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078409	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11656840	0.83[EUR][1000 genomes]
rs11658257	0.86[ASN][1000 genomes]
rs11869491	0.81[EUR][1000 genomes]
rs11869536	0.83[EUR][1000 genomes]
rs11870660	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11871231	0.81[EUR][1000 genomes]
rs11871899	0.82[EUR][1000 genomes]
rs12150369	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12452219	0.81[EUR][1000 genomes]
rs12452254	0.82[EUR][1000 genomes]
rs12600546	0.84[EUR][1000 genomes]
rs12603148	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12940282	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2350977	0.80[EUR][1000 genomes]
rs28428991	0.83[EUR][1000 genomes]
rs28537385	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2955350	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955352	0.80[ASN][1000 genomes]
rs2955353	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955354	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955359	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955369	0.88[ASN][1000 genomes]
rs2955370	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955372	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955377	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2955378	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2955380	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955381	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2955384	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2955385	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3935505	0.92[ASN][1000 genomes]
rs3935506	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4072738	0.81[EUR][1000 genomes]
rs4072739	0.81[EUR][1000 genomes]
rs4077198	0.83[EUR][1000 genomes]
rs4077828	0.83[EUR][1000 genomes]
rs4244602	0.82[EUR][1000 genomes]
rs4257260	0.84[EUR][1000 genomes]
rs4299203	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4341796	0.81[EUR][1000 genomes]
rs4343339	0.83[EUR][1000 genomes]
rs4365348	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4368210	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4413022	0.84[EUR][1000 genomes]
rs4414547	0.84[EUR][1000 genomes]
rs4459604	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4470201	0.83[EUR][1000 genomes]
rs4506969	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4534911	0.82[EUR][1000 genomes]
rs4553680	0.82[EUR][1000 genomes]
rs4584886	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4616340	0.84[EUR][1000 genomes]
rs4635395	0.96[AFR][1000 genomes]
rs4924832	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4925126	0.80[EUR][1000 genomes]
rs4925129	0.82[EUR][1000 genomes]
rs4925130	0.82[EUR][1000 genomes]
rs4925133	0.90[EUR][1000 genomes]
rs4925135	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5002487	0.82[EUR][1000 genomes]
rs57728924	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59304093	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62064156	0.82[EUR][1000 genomes]
rs62064158	0.84[EUR][1000 genomes]
rs62072048	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62072050	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502622	0.83[EUR][1000 genomes]
rs6502624	0.83[EUR][1000 genomes]
rs6502626	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6502627	0.84[EUR][1000 genomes]
rs6502631	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6502632	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6502633	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6502634	0.86[ASN][1000 genomes]
rs66531105	0.83[EUR][1000 genomes]
rs67253360	0.83[EUR][1000 genomes]
rs7207043	0.81[EUR][1000 genomes]
rs7207395	0.81[EUR][1000 genomes]
rs7207461	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7207821	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209003	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7212167	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7213225	0.84[EUR][1000 genomes]
rs7214002	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7214536	0.84[EUR][1000 genomes]
rs7215524	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7219320	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7222480	0.82[EUR][1000 genomes]
rs7223696	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7224047	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7406982	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7503738	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8065416	0.83[EUR][1000 genomes]
rs8065970	0.84[EUR][1000 genomes]
rs8066982	0.84[EUR][1000 genomes]
rs8068175	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8068820	0.84[EUR][1000 genomes]
rs8069811	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8070722	0.83[EUR][1000 genomes]
rs8070731	0.85[ASN][1000 genomes]
rs8070748	0.84[EUR][1000 genomes]
rs8071238	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8073001	0.83[EUR][1000 genomes]
rs8075189	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8076747	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs8077530	0.81[EUR][1000 genomes]
rs8078105	0.82[EUR][1000 genomes]
rs8078138	0.81[EUR][1000 genomes]
rs8078583	0.81[EUR][1000 genomes]
rs8080602	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8080823	0.82[EUR][1000 genomes]
rs9635697	0.84[EUR][1000 genomes]
rs9635698	0.83[EUR][1000 genomes]
rs9890341	0.83[EUR][1000 genomes]
rs9896837	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897761	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9899355	0.80[EUR][1000 genomes]
rs9904163	0.83[EUR][1000 genomes]
rs9905284	0.84[EUR][1000 genomes]
rs9908832	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9911850	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9912096	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9912895	0.83[EUR][1000 genomes]
rs9913277	0.82[EUR][1000 genomes]
rs9913724	0.82[EUR][1000 genomes]
rs9914127	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4471742	AC122129.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876400-17881600	Weak transcription	Spleen	Spleen
2	chr17:17876400-17884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:17876400-17888600	Weak transcription	Lung	lung
4	chr17:17876400-17903200	Weak transcription	Gastric	stomach
5	chr17:17876600-17879000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:17876600-17879400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:17876600-17880200	Weak transcription	Pancreas	Pancrea
8	chr17:17876600-17883400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr17:17876600-17884800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
11	chr17:17876800-17878200	Weak transcription	A549	lung
12	chr17:17876800-17878200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr17:17876800-17878400	Weak transcription	Primary B cells from cord blood	blood
14	chr17:17876800-17878800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:17876800-17880200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:17876800-17880200	Weak transcription	Fetal Stomach	stomach
17	chr17:17876800-17880600	Weak transcription	Placenta	Placenta
18	chr17:17876800-17882200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr17:17876800-17883000	Weak transcription	Stomach Mucosa	stomach
20	chr17:17876800-17884400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:17876800-17884600	Weak transcription	Brain Angular Gyrus	brain
22	chr17:17876800-17884600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:17876800-17891800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
25	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:17877000-17877800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr17:17877000-17878000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr17:17877000-17879000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:17877000-17880800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr17:17877000-17880800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:17877000-17881400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr17:17877000-17882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:17877000-17886400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:17877000-17886400	Weak transcription	NHEK	skin
35	chr17:17877000-17887000	Weak transcription	Brain Anterior Caudate	brain
36	chr17:17877000-17888000	Weak transcription	Ovary	ovary
37	chr17:17877000-17891000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:17877000-17891800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr17:17877000-17900000	Weak transcription	Fetal Intestine Small	intestine
40	chr17:17877200-17881800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:17877200-17891200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr17:17877200-17891400	Weak transcription	Fetal Muscle Leg	muscle
43	chr17:17877600-17880000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:17877600-17893200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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