Variant report

Variant	rs1984840
Chromosome Location	chr6:29640039-29640040
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	chr6:29634001..29636635-chr6:29639490..29642126,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1122947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079898	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2262263	0.81[ASN][1000 genomes]
rs2517913	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2535245	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535260	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735063	0.87[EUR][1000 genomes]
rs2747425	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2747453	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747455	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs29231	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29273	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2982837	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095287	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129041	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129074	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129087	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129090	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131879	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131881	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131882	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6456993	0.89[EUR][1000 genomes]
rs6941117	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7738159	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7774576	0.81[ASN][1000 genomes]
rs7776296	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9257931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258093	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258094	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258102	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258106	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258111	0.81[ASN][1000 genomes]
rs9258114	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258126	0.87[EUR][1000 genomes]
rs9258127	0.87[EUR][1000 genomes]
rs9258131	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1984840	HLA-A	cis	Artery Tibial	GTEx
rs1984840	HLA-A	cis	Thyroid	GTEx
rs1984840	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1984840	HLA-A	cis	Nerve Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:29631400-29640200	Weak transcription	NHEK	skin
4	chr6:29634600-29641000	Weak transcription	Brain Anterior Caudate	brain
5	chr6:29634600-29642000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:29636400-29643800	Weak transcription	Fetal Heart	heart
7	chr6:29636600-29642000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:29636600-29644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:29637000-29644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:29638800-29644400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:29639200-29640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:29639400-29640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:29639600-29641400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:29639600-29641400	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:29639600-29641400	Weak transcription	Brain Substantia Nigra	brain
16	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:29639800-29643400	Weak transcription	Brain Cingulate Gyrus	brain

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