Variant report

Variant	rs3799094
Chromosome Location	chr6:70080512-70080513
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:70078631..70080684-chr6:70081280..70084029,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10485251	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs11751775	0.87[ASW][hapmap];0.83[TSI][hapmap]
rs11755891	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11758564	0.98[EUR][1000 genomes]
rs11964197	1.00[CEU][hapmap]
rs12173971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12525747	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12526777	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16900663	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16900676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17691995	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs1952435	0.81[CHD][hapmap]
rs2296974	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2296975	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs2880923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58607458	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6907374	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6912952	0.87[ASW][hapmap];0.82[EUR][1000 genomes]
rs73471339	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73471350	0.92[EUR][1000 genomes]
rs9346273	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9351751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.89[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	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv432919	chr6:69873179-70221322	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv463149	chr6:70007450-70097588	Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv603635	chr6:70007450-70097588	Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799094	SNORD41	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70049600-70080600	Weak transcription	Fetal Brain Male	brain
2	chr6:70054600-70098600	Weak transcription	Brain Anterior Caudate	brain
3	chr6:70054600-70100600	Weak transcription	Brain Angular Gyrus	brain
4	chr6:70054800-70080600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:70059200-70083200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:70063000-70080600	Weak transcription	Brain Germinal Matrix	brain
7	chr6:70066600-70080600	Weak transcription	Fetal Brain Female	brain
8	chr6:70072600-70080600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:70078600-70081200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:70078800-70081200	Enhancers	Fetal Lung	lung
11	chr6:70079400-70081000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:70079800-70080600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:70080000-70081000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:70080000-70081400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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