Variant report

Variant	rs9468344
Chromosome Location	chr6:28309569-28309570
allele	G/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	chr6:28309225-28309586	K562	blood:	n/a	n/a

Variant related genes	Relation type
ZSCAN31	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs1016070	0.86[CHB][hapmap]
rs1150711	0.81[TSI][hapmap]
rs12000	0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs12180820	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893947	0.81[CHD][hapmap]
rs16893970	0.81[CHD][hapmap]
rs1997660	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2021745	0.86[CHB][hapmap]
rs2108926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531813	0.86[CHB][hapmap]
rs2531814	0.86[CHB][hapmap]
rs2859372	0.86[CHB][hapmap]
rs2859373	0.86[CHB][hapmap]
rs2859374	0.86[CHB][hapmap]
rs4713158	0.86[EUR][1000 genomes]
rs6456815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936644	0.92[ASN][1000 genomes]
rs6942030	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707907	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs758398	0.86[CHB][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772827	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs853683	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs853690	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs853693	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs9468333	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs9468334	0.89[ASN][1000 genomes]

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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9468344	ZSCAN23	cis	parietal	SCAN
rs9468344	AL022393.7	cis	Nerve Tibial	GTEx
rs9468344	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468344	ZKSCAN3	cis	cerebellum	SCAN
rs9468344	ZKSCAN3	cis	parietal	SCAN
rs9468344	ZNF323	cis	parietal	SCAN
rs9468344	HLA-H	cis	multi-tissue	Pritchard
rs9468344	NKAPL	cis	parietal	SCAN
rs9468344	AL022393.7	cis	Esophagus Muscularis	GTEx
rs9468344	ZNF192	cis	cerebellum	SCAN
rs9468344	RP5-874C20.3	cis	Thyroid	GTEx
rs9468344	AL022393.7	cis	Heart Left Ventricle	GTEx
rs9468344	ZNF187	cis	cerebellum	SCAN
rs9468344	HIST1H2BN	cis	cerebellum	SCAN
rs9468344	AL022393.7	cis	Muscle Skeletal	GTEx
rs9468344	ZSCAN23	cis	cerebellum	SCAN
rs9468344	ZSCAN31	cis	lung	GTEx
rs9468344	HIST1H2BO	cis	parietal	SCAN
rs9468344	ZSCAN23	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 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	chr6:28309400-28314800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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