Variant report

Variant	rs9380090
Chromosome Location	chr6:28758828-28758829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28692257..28693945-chr6:28757387..28759135,2	K562	blood:
2	chr6:28758828..28759555-chr9:136657868..136658790,2	MCF-7	breast:
3	chr6:28757752..28760408-chr6:28765977..28767794,2	K562	blood:
4	chr6:28739775..28742884-chr6:28756307..28759477,3	K562	blood:
5	chr6:28752766..28756379-chr6:28756550..28759154,4	K562	blood:
6	chr6:28756425..28760621-chr6:28761088..28764506,5	K562	blood:
7	chr6:28686813..28689115-chr6:28758010..28760174,2	K562	blood:
8	chr6:28756573..28759569-chr6:28769791..28772080,4	K562	blood:
9	chr6:28695047..28697144-chr6:28756622..28759292,2	K562	blood:
10	chr6:28725484..28727930-chr6:28757614..28759136,2	K562	blood:
11	chr6:28734776..28737188-chr6:28758091..28759724,2	K562	blood:
12	chr6:28757312..28759023-chr6:28889870..28891731,2	K562	blood:
13	chr6:28755863..28759570-chr6:28911484..28914475,3	K562	blood:
14	chr6:28743173..28744938-chr6:28758816..28760398,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000221191	Chromatin interaction
ENSG00000265764	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28381660	0.84[AFR][1000 genomes]
rs9257158	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9257181	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9257186	0.82[AFR][1000 genomes]
rs9378107	0.83[AFR][1000 genomes]
rs9380092	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9380090	ZSCAN16	cis	parietal	SCAN
rs9380090	RFP	cis	multi-tissue	Pritchard
rs9380090	PRSS16	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28756400-28759200	Active TSS	A549	lung
2	chr6:28756600-28759000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:28756800-28759000	Active TSS	Placenta	Placenta
4	chr6:28756800-28759000	Active TSS	K562	blood
5	chr6:28756800-28759200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28757200-28759000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:28757400-28759000	Active TSS	GM12878-XiMat	blood
8	chr6:28757400-28759200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:28757600-28759000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:28757600-28759000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:28757600-28759200	Active TSS	Hela-S3	cervix
12	chr6:28758200-28759000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:28758200-28761600	Weak transcription	HMEC	breast
14	chr6:28758400-28761600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:28758400-28761800	Weak transcription	HSMMtube	muscle
16	chr6:28758600-28759000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr6:28758600-28759000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr6:28758600-28759000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr6:28758600-28759000	Flanking Active TSS	Osteobl	bone
20	chr6:28758600-28759200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:28758600-28759600	Flanking Active TSS	HepG2	liver
22	chr6:28758800-28759000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
23	chr6:28758800-28759000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
24	chr6:28758800-28759200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:28758800-28759200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:28758800-28759200	Enhancers	NHEK	skin
27	chr6:28758800-28761800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:28758800-28761800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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