Variant report

Variant	rs17301128
Chromosome Location	chr6:28308034-28308035
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr6:28307991-28308466	K562	blood:	n/a	n/a
2	POLR2A	chr6:28307826-28308288	K562	blood:	n/a	n/a
3	KAP1	chr6:28307937-28308888	K562	blood:	n/a	n/a
4	MAFK	chr6:28307850-28308078	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
2	chr6:28306214..28308475-chr6:28356791..28358478,2	K562	blood:
3	chr6:28233528..28236356-chr6:28305759..28308573,2	K562	blood:
4	chr6:28220144..28224072-chr6:28306303..28309254,3	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000198315	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1119211	1.00[CEU][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11756111	1.00[JPT][hapmap]
rs11758148	1.00[JPT][hapmap]
rs11758337	1.00[JPT][hapmap]
rs11970439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13210258	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1474589	1.00[JPT][hapmap]
rs16893937	1.00[JPT][hapmap]
rs17312661	0.94[CEU][hapmap]
rs17776284	1.00[JPT][hapmap]
rs2185955	1.00[JPT][hapmap]
rs2235358	1.00[JPT][hapmap]
rs2235359	1.00[JPT][hapmap]
rs2299031	1.00[JPT][hapmap]
rs2799081	0.81[EUR][1000 genomes]
rs3800326	1.00[JPT][hapmap]
rs56131013	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456814	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6456816	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6903652	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903823	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921919	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6922111	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7766356	0.83[CEU][hapmap]
rs7769054	1.00[JPT][hapmap]
rs9468350	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs993619	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17301128	ZSCAN23	cis	Muscle Skeletal	GTEx
rs17301128	HLA-A	cis	multi-tissue	Pritchard
rs17301128	AL022393.7	cis	Muscle Skeletal	GTEx
rs17301128	BTN3A2	cis	multi-tissue	Pritchard
rs17301128	HLA-H	cis	multi-tissue	Pritchard
rs17301128	ZSCAN23	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28304400-28317400	Weak transcription	Pancreas	Pancrea
2	chr6:28304800-28317200	Weak transcription	Aorta	Aorta
3	chr6:28305000-28310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:28305000-28317200	Weak transcription	Brain Anterior Caudate	brain
5	chr6:28305000-28317200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:28305200-28311800	Weak transcription	Brain Angular Gyrus	brain
7	chr6:28305200-28313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:28305200-28317000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:28305200-28317000	Weak transcription	NHEK	skin
10	chr6:28305200-28317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:28305200-28317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:28305200-28317200	Weak transcription	HSMMtube	muscle
13	chr6:28305800-28317200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:28307600-28309400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:28308000-28308800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--

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