Variant report

Variant	rs62392953
Chromosome Location	chr6:29647515-29647516
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs16895218	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16895757	1.00[AFR][1000 genomes]
rs17184661	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29233	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29254	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3117313	0.97[ASN][1000 genomes]
rs3888722	1.00[AFR][1000 genomes]
rs3906306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4085262	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4085264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143366	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55661776	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55672647	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55693745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55791644	1.00[AFR][1000 genomes]
rs55792521	0.82[ASN][1000 genomes]
rs55884048	1.00[AFR][1000 genomes]
rs55933609	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56044823	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56101454	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56155978	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56172386	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56269224	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56287651	1.00[AFR][1000 genomes]
rs56290866	1.00[AFR][1000 genomes]
rs56392172	1.00[AFR][1000 genomes]
rs62391766	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62391767	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62391768	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62391770	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62391785	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62391786	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62391801	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62391819	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62391822	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62391833	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62391835	1.00[AFR][1000 genomes]
rs62391842	1.00[AFR][1000 genomes]
rs62391843	1.00[AFR][1000 genomes]
rs62391844	1.00[AFR][1000 genomes]
rs62391850	1.00[AFR][1000 genomes]
rs62391851	1.00[AFR][1000 genomes]
rs62392946	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62394668	1.00[AFR][1000 genomes]
rs62394669	1.00[AFR][1000 genomes]
rs62394670	1.00[AFR][1000 genomes]
rs67382831	1.00[AFR][1000 genomes]
rs71550159	1.00[AFR][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62392953	HLA-U	cis	Skin Sun Exposed Lower leg	GTEx
rs62392953	HLA-U	cis	Artery Tibial	GTEx
rs62392953	HLA-U	cis	lung	GTEx
rs62392953	HLA-H	cis	Artery Tibial	GTEx
rs62392953	HLA-U	cis	Whole Blood	GTEx
rs62392953	HLA-H	cis	Artery Aorta	GTEx
rs62392953	HLA-U	cis	Nerve Tibial	GTEx
rs62392953	HLA-U	cis	Thyroid	GTEx
rs62392953	HLA-U	cis	Artery Aorta	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29643000-29648800	Enhancers	HMEC	breast
3	chr6:29643200-29648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29643400-29648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:29643800-29647600	Enhancers	Fetal Heart	heart
6	chr6:29644600-29647800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:29644800-29647600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:29644800-29648000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:29644800-29648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:29645000-29648000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:29645200-29648200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:29645200-29648400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:29645800-29648200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:29646000-29648400	Flanking Active TSS	NHEK	skin
15	chr6:29646000-29648800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:29646000-29651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:29646200-29651400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:29646200-29651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:29646400-29648400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:29646600-29647600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:29646800-29651400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:29647000-29649600	Weak transcription	Spleen	Spleen
23	chr6:29647000-29651400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:29647000-29651400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:29647400-29648200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:29647400-29651600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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