Variant report

Variant	rs533996
Chromosome Location	chr6:163486210-163486211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1536034	0.84[EUR][1000 genomes]
rs2985663	0.95[EUR][1000 genomes]
rs4709673	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs471067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485964	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs492214	0.97[ASN][1000 genomes]
rs501276	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs502478	0.95[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs503173	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs526117	0.95[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs529106	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs532302	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs542381	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs545584	0.95[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs545846	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs546769	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs561440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562299	0.94[ASN][1000 genomes]
rs566169	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57432193	0.83[EUR][1000 genomes]
rs577874	0.94[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs579834	0.88[EUR][1000 genomes]
rs9355420	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917926	chr6:162646457-163609259	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv529089	chr6:163129464-163516451	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1030116	chr6:163273707-163525678	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020900	chr6:163302262-163517812	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv916587	chr6:163337791-163606120	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1021433	chr6:163375760-163509866	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv605187	chr6:163448750-163496289	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1034556	chr6:163449712-163488528	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv538525	chr6:163449712-163488528	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs533996	FNDC1	cis	parietal	SCAN
rs533996	QKI	cis	parietal	SCAN
rs533996	IGF2R	cis	cerebellum	SCAN
rs533996	MRPL18	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163479400-163488200	Weak transcription	Gastric	stomach
2	chr6:163482400-163488600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:163486000-163486400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:163486000-163487600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:163486200-163486600	Enhancers	Brain Anterior Caudate	brain
6	chr6:163486200-163486800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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