Variant report

Variant	rs2747425
Chromosome Location	chr6:29646790-29646791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:29646674-29647037	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ZFP57	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1122947	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1984840	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2079898	0.86[EUR][1000 genomes]
rs2517913	0.82[EUR][1000 genomes]
rs2535245	0.84[EUR][1000 genomes]
rs2535246	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2735063	0.82[EUR][1000 genomes]
rs2747453	0.90[EUR][1000 genomes]
rs2747455	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs29231	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs29273	0.84[EUR][1000 genomes]
rs2982837	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095287	0.85[EUR][1000 genomes]
rs3129041	0.83[EUR][1000 genomes]
rs3129074	0.83[EUR][1000 genomes]
rs3129087	0.81[EUR][1000 genomes]
rs3129090	0.90[EUR][1000 genomes]
rs3131879	0.85[EUR][1000 genomes]
rs3131881	0.86[EUR][1000 genomes]
rs3131882	0.84[EUR][1000 genomes]
rs6456993	0.84[EUR][1000 genomes]
rs6941117	0.84[EUR][1000 genomes]
rs7776296	0.83[EUR][1000 genomes]
rs9257931	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9258093	0.84[EUR][1000 genomes]
rs9258094	0.83[EUR][1000 genomes]
rs9258102	0.84[EUR][1000 genomes]
rs9258106	0.81[EUR][1000 genomes]
rs9258114	0.84[EUR][1000 genomes]
rs9258126	0.82[EUR][1000 genomes]
rs9258127	0.82[EUR][1000 genomes]
rs9258131	0.82[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2747425	HLA-A	cis	Artery Tibial	GTEx
rs2747425	HLA-A	cis	Thyroid	GTEx
rs2747425	HLA-A	cis	Nerve Tibial	GTEx
rs2747425	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:29643000-29648800	Enhancers	HMEC	breast
4	chr6:29643200-29648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:29643400-29648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:29643800-29647600	Enhancers	Fetal Heart	heart
7	chr6:29644600-29647800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:29644800-29647400	Enhancers	Hela-S3	cervix
9	chr6:29644800-29647600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:29644800-29648000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:29644800-29648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:29645000-29646800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:29645000-29648000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:29645200-29648200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:29645200-29648400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:29645600-29647000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:29645800-29648200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:29646000-29648400	Flanking Active TSS	NHEK	skin
19	chr6:29646000-29648800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:29646000-29651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:29646200-29646800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:29646200-29651400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:29646200-29651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:29646400-29648400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:29646600-29647000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:29646600-29647600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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