Variant report

Variant	rs6795936
Chromosome Location	chr3:118681771-118681772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11927719	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487299	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489856	0.88[EUR][1000 genomes]
rs12636639	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs1369583	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs16829163	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1879552	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2110368	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2110369	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2160052	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2192365	0.82[ASW][hapmap];0.95[GIH][hapmap];0.87[MKK][hapmap]
rs2215811	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs2866317	0.89[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs36052974	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55758895	0.90[AFR][1000 genomes]
rs58464946	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58521606	0.83[AFR][1000 genomes]
rs6765168	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6782002	0.86[TSI][hapmap]
rs6802658	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs73183699	0.88[EUR][1000 genomes]
rs73185803	0.88[EUR][1000 genomes]
rs7610212	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638463	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7651619	0.94[ASW][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs9848979	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs9854506	0.89[CEU][hapmap];0.88[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6795936	IGSF11	cis	cerebellum	SCAN
rs6795936	IGSF11	cis	parietal	SCAN
rs6795936	GOLGB1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118675600-118684800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:118676800-118684000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:118679000-118688200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:118680000-118683800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:118680200-118681800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:118680200-118684600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:118680200-118684600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:118680200-118684800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:118680200-118686600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:118680200-118686600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:118680200-118688200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:118680200-118688200	Weak transcription	Ovary	ovary
13	chr3:118680800-118681800	Weak transcription	Brain Anterior Caudate	brain
14	chr3:118681200-118694000	Enhancers	Brain Substantia Nigra	brain
15	chr3:118681400-118683400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:118681400-118683400	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:118681400-118684000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:118681400-118690000	Enhancers	Brain Hippocampus Middle	brain
19	chr3:118681600-118682200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:118681600-118683400	Enhancers	Brain Angular Gyrus	brain

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