Variant report

Variant	rs3733460
Chromosome Location	chr4:147096994-147096995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147096162..147099903-chr4:147161380..147165203,4	MCF-7	breast:
2	chr4:147095588..147099041-chr4:147101501..147104102,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164167	Chromatin interaction
ENSG00000251010	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10519776	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1079476	0.89[ASN][1000 genomes]
rs11100919	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11721367	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11721873	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11723069	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11728609	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729787	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11730306	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11733347	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152657	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152692	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152709	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17021106	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17021186	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17021217	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17756234	0.80[EUR][1000 genomes]
rs17757522	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17757685	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17757715	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17758092	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17758396	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17758420	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17814023	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17814065	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17814503	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17814598	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1865531	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1865532	0.80[EUR][1000 genomes]
rs2068009	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115796	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115797	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163171	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2164280	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28420466	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733458	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756081	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756082	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756083	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775498	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815967	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4282199	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55736910	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56279747	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56333123	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56393662	0.89[ASN][1000 genomes]
rs62326797	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62326801	0.85[ASN][1000 genomes]
rs62326802	0.85[ASN][1000 genomes]
rs62326804	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62326848	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537401	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537402	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537403	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816161	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6820462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821066	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821444	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821479	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821863	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824313	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839123	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839141	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844381	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6858813	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72727944	0.83[ASN][1000 genomes]
rs72727952	0.89[ASN][1000 genomes]
rs7657269	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7665079	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7745	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs919482	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs919483	0.85[EUR][1000 genomes];0.91[ASN][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	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3733460	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs3733460	RP11-6L6.2	cis	Artery Tibial	GTEx
rs3733460	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3733460	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs3733460	RP11-6L6.2	cis	Whole Blood	GTEx
rs3733460	RP11-6L6.2	cis	Thyroid	GTEx
rs3733460	RP11-6L6.2	cis	lung	GTEx
rs3733460	RP11-6L6.2	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147096200-147097200	Active TSS	HepG2	liver
2	chr4:147096200-147097400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:147096200-147098000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr4:147096200-147098000	Active TSS	Rectal Smooth Muscle	rectum
5	chr4:147096400-147097400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:147096400-147097400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:147096400-147097400	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr4:147096400-147097600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:147096400-147097600	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr4:147096400-147097600	Active TSS	Fetal Brain Male	brain
11	chr4:147096400-147097600	Active TSS	Fetal Brain Female	brain
12	chr4:147096400-147097600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr4:147096400-147097600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr4:147096400-147097800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr4:147096400-147097800	Active TSS	Duodenum Mucosa	Duodenum
16	chr4:147096400-147097800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr4:147096400-147097800	Active TSS	NHDF-Ad	bronchial
18	chr4:147096400-147098000	Active TSS	Brain Substantia Nigra	brain
19	chr4:147096400-147098000	Active TSS	A549	lung
20	chr4:147096400-147098000	Active TSS	K562	blood
21	chr4:147096400-147098200	Active TSS	NH-A	brain
22	chr4:147096400-147098400	Active TSS	GM12878-XiMat	blood
23	chr4:147096600-147097000	Active TSS	Primary hematopoietic stem cells	blood
24	chr4:147096600-147097000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:147096600-147097200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr4:147096600-147097400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:147096600-147097400	Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr4:147096600-147097400	Active TSS	Primary B cells from peripheral blood	blood
29	chr4:147096600-147097400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:147096600-147097400	Active TSS	Adipose Nuclei	Adipose
31	chr4:147096600-147097400	Active TSS	Liver	Liver
32	chr4:147096600-147097400	Active TSS	Brain Angular Gyrus	brain
33	chr4:147096600-147097600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr4:147096600-147097600	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr4:147096600-147097600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr4:147096600-147097600	Active TSS	Brain Anterior Caudate	brain
37	chr4:147096600-147097600	Active TSS	Brain Hippocampus Middle	brain
38	chr4:147096600-147097600	Active TSS	Fetal Heart	heart
39	chr4:147096600-147097600	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr4:147096600-147097600	Active TSS	Osteobl	bone
41	chr4:147096600-147097800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:147096600-147097800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:147096600-147097800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr4:147096600-147097800	Active TSS	Brain Cingulate Gyrus	brain
45	chr4:147096600-147097800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr4:147096600-147097800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr4:147096600-147097800	Active TSS	Fetal Intestine Large	intestine
48	chr4:147096600-147097800	Active TSS	Fetal Muscle Trunk	muscle
49	chr4:147096600-147097800	Active TSS	HSMMtube	muscle
50	chr4:147096600-147097800	Active TSS	NHEK	skin

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