Variant report

Variant	rs385492
Chromosome Location	chr6:29649547-29649548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2394658	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2535253	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2747449	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2894113	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094736	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3116807	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3116808	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3116809	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3116810	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3117317	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129053	0.80[AFR][1000 genomes]
rs3129057	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129091	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131885	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs427236	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs385492	ZFP57	cis	lung	GTEx
rs385492	ZFP57	cis	Whole Blood	GTEx
rs385492	IFITM4P	cis	Thyroid	GTEx
rs385492	HIST1H2AM	cis	parietal	SCAN
rs385492	HLA-A	cis	lymphoblastoid	GTEx
rs385492	IFITM4P	cis	Artery Tibial	GTEx
rs385492	ZFP57	cis	Thyroid	GTEx
rs385492	ZFP57	cis	lymphoblastoid	seeQTL
rs385492	ZFP57	cis	Adipose Subcutaneous	GTEx
rs385492	FLJ35429	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 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	chr6:29647000-29649600	Weak transcription	Spleen	Spleen
7	chr6:29647000-29651400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:29647000-29651400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:29647400-29651600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:29648000-29651400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:29648200-29651400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:29648800-29651400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:29648800-29662600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:29649000-29651200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:29649200-29652000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:29649200-29655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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