Variant report

Variant	rs6912584
Chromosome Location	chr6:28309590-28309591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs1119211	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11756111	0.86[GIH][hapmap];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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13210258	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1474589	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs16893937	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs17301128	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]
rs17312661	0.94[CEU][hapmap]
rs17776284	1.00[JPT][hapmap]
rs2185955	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2235358	1.00[JPT][hapmap]
rs2235359	0.86[GIH][hapmap];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];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456814	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6456816	0.83[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];1.00[AFR][1000 genomes];0.92[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];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921919	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6922111	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7766356	0.83[CEU][hapmap]
rs7769054	1.00[JPT][hapmap]
rs9468350	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs993619	0.81[GIH][hapmap];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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6912584	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6912584	AL022393.7	cis	Muscle Skeletal	GTEx
rs6912584	ZKSCAN3	cis	parietal	SCAN
rs6912584	ZNF192	cis	cerebellum	SCAN
rs6912584	ZSCAN23	cis	parietal	SCAN
rs6912584	ZNF323	cis	parietal	SCAN
rs6912584	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs6912584	ZSCAN23	cis	Muscle Skeletal	GTEx
rs6912584	LRRC16A	cis	parietal	SCAN
rs6912584	ZSCAN23	cis	Artery Tibial	GTEx
rs6912584	HIST1H2BM	cis	cerebellum	SCAN
rs6912584	ZSCAN23	cis	cerebellum	SCAN
rs6912584	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

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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