Variant report

Variant	rs4869764
Chromosome Location	chr6:150211828-150211829
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	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1334510	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2095376	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2342767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342768	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2342769	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2342770	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458704	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4869763	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870116	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6557133	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6933882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935829	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6939761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742692	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742993	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744821	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7747435	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7747457	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7756850	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757972	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757984	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758020	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758033	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7763719	0.83[EUR][1000 genomes]
rs7763849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7764376	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767588	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7767592	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7768626	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7768665	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769118	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771014	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774787	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322225	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322228	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9371215	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9371223	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9371504	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371505	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371533	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9371541	0.94[ASN][1000 genomes]
rs9371542	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9371544	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9383577	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383584	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383912	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383914	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383921	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383940	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9397058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9397398	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9397420	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9397434	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478192	0.81[EUR][1000 genomes]
rs9968871	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9969044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4869764	RAET1G	cis	Esophagus Mucosa	GTEx
rs4869764	RAET1E	cis	Nerve Tibial	GTEx
rs4869764	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs4869764	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4869764	LRP11	cis	Adipose Subcutaneous	GTEx
rs4869764	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs4869764	RAET1G	cis	Artery Tibial	GTEx
rs4869764	RP11-350J20.5	cis	Thyroid	GTEx
rs4869764	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs4869764	RP11-350J20.9	cis	lung	GTEx
rs4869764	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs4869764	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs4869764	RAET1G	cis	Thyroid	GTEx
rs4869764	RP11-350J20.5	cis	Artery Tibial	GTEx
rs4869764	RP11-350J20.5	cis	lung	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
2	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:150208400-150212600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:150208400-150212600	Flanking Active TSS	Hela-S3	cervix
6	chr6:150209200-150212200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr6:150209200-150212800	Enhancers	A549	lung
8	chr6:150209600-150215800	Weak transcription	Adipose Nuclei	Adipose
9	chr6:150209600-150216000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:150210600-150212800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:150211200-150212000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr6:150211200-150212600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:150211400-150212000	Enhancers	Psoas Muscle	Psoas
15	chr6:150211400-150212200	Flanking Active TSS	HMEC	breast
16	chr6:150211400-150212200	Flanking Active TSS	NHEK	skin
17	chr6:150211400-150212400	Flanking Active TSS	HSMMtube	muscle
18	chr6:150211400-150212600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:150211400-150212600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:150211600-150212000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:150211600-150212000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:150211600-150212000	Enhancers	Fetal Muscle Trunk	muscle
23	chr6:150211600-150212000	Enhancers	Placenta	Placenta
24	chr6:150211600-150212000	Flanking Active TSS	HSMM	muscle
25	chr6:150211600-150212200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:150211600-150212600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:150211600-150212600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:150211600-150212800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:150211600-150212800	Enhancers	NHDF-Ad	bronchial
30	chr6:150211600-150212800	Enhancers	Osteobl	bone
31	chr6:150211800-150212000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:150211800-150212400	Enhancers	Fetal Muscle Leg	muscle
33	chr6:150211800-150212600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:150211800-150212600	Enhancers	Esophagus	oesophagus

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