Variant report

Variant	rs3129053
Chromosome Location	chr6:29650004-29650005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1018935	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535235	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535236	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747434	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747436	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747442	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2747443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2982839	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095286	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095288	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095289	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3117291	0.86[AMR][1000 genomes]
rs3117292	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3117293	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117294	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129045	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129054	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3129057	0.84[AFR][1000 genomes]
rs3131846	0.82[EUR][1000 genomes]
rs3131847	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs385354	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs385492	0.80[AFR][1000 genomes]
rs430133	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	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
4	nsv10808	chr6:29648051-29653183	Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3129053	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3129053	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29646000-29651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:29646200-29651400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:29646200-29651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:29646800-29651400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:29647000-29651400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:29647000-29651400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:29647400-29651600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:29648000-29651400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:29648200-29651400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:29648800-29651400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:29648800-29662600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:29649000-29651200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:29649200-29652000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:29649200-29655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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