Variant report

Variant	rs10455273
Chromosome Location	chr6:74005073-74005074
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:73927031-73938730..6:74000304-74012200	K562	blood:
2	chr6:74000906..74002933-chr6:74004885..74007636,2	K562	blood:
3	6:74000304-74012200..6:74062967-74076046	GM12878	blood:
4	chr6:74003554..74006209-chr6:74017502..74020116,3	MCF-7	breast:
5	chr6:73996124..73998490-chr6:74004776..74007375,2	K562	blood:
6	6:74000304-74012200..6:74160392-74184826	K562	blood:
7	chr6:74004356..74006447-chr6:74007681..74009584,2	K562	blood:
8	6:74000304-74012200..6:74078047-74099067	H1-hESC	embryonic stem cell:	embryo
9	6:74000304-74012200..6:74099986-74112890	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000135297	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000256980	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000234882	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000135314	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000231332	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10455092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10455274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1066687	0.93[ASN][1000 genomes]
rs12153835	0.95[ASN][1000 genomes]
rs12203663	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208781	0.96[ASN][1000 genomes]
rs12210531	0.94[ASN][1000 genomes]
rs12216162	0.96[ASN][1000 genomes]
rs12526643	0.93[ASN][1000 genomes]
rs12529624	0.96[ASN][1000 genomes]
rs12529658	0.96[ASN][1000 genomes]
rs12530029	0.92[ASN][1000 genomes]
rs12530079	0.96[ASN][1000 genomes]
rs13194683	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13212903	0.96[ASN][1000 genomes]
rs13213885	0.96[ASN][1000 genomes]
rs13219250	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555443	0.96[ASN][1000 genomes]
rs1869559	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970551	0.96[ASN][1000 genomes]
rs1974368	0.94[ASN][1000 genomes]
rs2124004	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254630	0.96[ASN][1000 genomes]
rs2603471	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603472	0.82[EUR][1000 genomes]
rs2603473	0.93[EUR][1000 genomes]
rs2603474	0.84[EUR][1000 genomes]
rs2797086	0.93[ASN][1000 genomes]
rs28530192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2984129	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34246858	0.95[ASN][1000 genomes]
rs34531450	0.96[ASN][1000 genomes]
rs34637067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34821383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35664677	0.94[ASN][1000 genomes]
rs4706533	0.92[ASN][1000 genomes]
rs4706534	0.92[ASN][1000 genomes]
rs4708041	0.92[ASN][1000 genomes]
rs4708042	0.92[ASN][1000 genomes]
rs471270	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs471938	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502107	0.89[ASN][1000 genomes]
rs502282	0.96[ASN][1000 genomes]
rs509406	0.96[ASN][1000 genomes]
rs510551	0.91[ASN][1000 genomes]
rs511219	0.96[ASN][1000 genomes]
rs512366	0.91[ASN][1000 genomes]
rs555779	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57113415	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs573535	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576229	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579736	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61493410	0.89[ASN][1000 genomes]
rs62438232	0.96[ASN][1000 genomes]
rs62438233	0.96[ASN][1000 genomes]
rs62438235	0.96[ASN][1000 genomes]
rs62438239	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66984567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915004	0.92[EUR][1000 genomes]
rs6923111	0.88[ASN][1000 genomes]
rs6923734	0.95[ASN][1000 genomes]
rs7382700	0.91[ASN][1000 genomes]
rs7740081	0.92[ASN][1000 genomes]
rs7742847	0.96[ASN][1000 genomes]
rs7743609	0.96[ASN][1000 genomes]
rs7744174	0.92[ASN][1000 genomes]
rs7758047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759043	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7764719	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765618	0.96[ASN][1000 genomes]
rs7769905	0.94[ASN][1000 genomes]
rs7773619	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9800483	0.85[ASN][1000 genomes]
rs9800824	0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10455273	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx
rs10455273	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:73973600-74018600	Weak transcription	A549	lung
3	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:73974000-74009000	Weak transcription	HSMM	muscle
5	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:73974400-74008800	Weak transcription	NH-A	brain
7	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:73974600-74008600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:73974800-74008600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:73977400-74008800	Weak transcription	Fetal Brain Male	brain
11	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:73984800-74008600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:73985200-74008800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:73985400-74009000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:73985600-74008800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:73985600-74008800	Weak transcription	Thymus	Thymus
18	chr6:73985800-74006800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:73985800-74008800	Weak transcription	Ovary	ovary
20	chr6:73986400-74008600	Weak transcription	Fetal Brain Female	brain
21	chr6:73989000-74017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:73989800-74008800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:73992400-74013200	Weak transcription	GM12878-XiMat	blood
24	chr6:73994200-74018600	Weak transcription	Stomach Mucosa	stomach
25	chr6:73996000-74008600	Weak transcription	Fetal Heart	heart
26	chr6:73996000-74008600	Weak transcription	Fetal Kidney	kidney
27	chr6:73996000-74009800	Weak transcription	K562	blood
28	chr6:73996000-74015800	Weak transcription	Hela-S3	cervix
29	chr6:73999000-74008600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:74000600-74007800	Weak transcription	HMEC	breast
31	chr6:74000600-74008800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:74000800-74008400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:74000800-74009000	Weak transcription	Aorta	Aorta
34	chr6:74001000-74008200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:74001000-74008600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:74001000-74008800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:74001000-74008800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:74001000-74008800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:74001000-74008800	Weak transcription	Fetal Lung	lung
40	chr6:74001000-74009000	Weak transcription	Osteobl	bone
41	chr6:74001000-74017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:74001400-74007400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:74001600-74008800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr6:74001600-74008800	Weak transcription	Fetal Thymus	thymus
45	chr6:74001800-74008600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:74001800-74008600	Weak transcription	Brain Germinal Matrix	brain
47	chr6:74001800-74008600	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:74002000-74007000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:74002000-74008400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:74002000-74013000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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