Variant report

Variant	rs6782002
Chromosome Location	chr3:118624631-118624632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118621808..118624756-chr3:118628385..118630071,2	K562	blood:
2	chr3:118617035..118619644-chr3:118623950..118626298,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11927719	0.80[LWK][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes]
rs12489856	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1879552	0.81[AFR][1000 genomes]
rs2110368	0.86[TSI][hapmap]
rs2110369	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2160052	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2215811	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2866317	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs66601488	0.87[AFR][1000 genomes]
rs6795936	0.86[TSI][hapmap]
rs6802658	0.89[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73183699	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73185803	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9848979	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9854506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6782002	IGSF11	cis	cerebellum	SCAN
rs6782002	HSPBAP1	cis	cerebellum	SCAN
rs6782002	PDIA5	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118612200-118625600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:118614200-118625000	Weak transcription	Aorta	Aorta
3	chr3:118619800-118625000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:118619800-118651400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:118620200-118625400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:118620200-118627200	Weak transcription	Fetal Brain Female	brain
7	chr3:118620200-118663200	Weak transcription	Pancreas	Pancrea
8	chr3:118620400-118625200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:118621400-118626800	Weak transcription	A549	lung
10	chr3:118621800-118630200	Weak transcription	Brain Germinal Matrix	brain
11	chr3:118622000-118624800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:118622000-118644600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:118622200-118625000	Weak transcription	Ovary	ovary
14	chr3:118623000-118628800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:118623400-118627200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:118623400-118627400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:118623400-118628400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:118623400-118628400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:118623400-118628800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:118623400-118629200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:118624000-118631200	Weak transcription	Brain Anterior Caudate	brain
22	chr3:118624600-118626600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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