Variant report

Variant	rs3801969
Chromosome Location	chr7:106711492-106711493
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:106416730..106418779-chr7:106710743..106713465,2	K562	blood:

Variant related genes	Relation type
ENSG00000228742	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10281856	0.83[JPT][hapmap]
rs10953528	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11760261	0.83[JPT][hapmap]
rs11766415	0.83[CEU][hapmap]
rs12667954	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12669339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12674011	0.92[ASN][1000 genomes]
rs12705402	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12705403	0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs1860803	0.83[JPT][hapmap]
rs2158347	0.84[ASW][hapmap]
rs2237652	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2237654	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2237656	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2237657	0.81[ASN][1000 genomes]
rs2283037	0.90[ASN][1000 genomes]
rs2302453	0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap]
rs2395836	0.82[ASW][hapmap];0.82[MKK][hapmap]
rs257384	0.82[ASW][hapmap];0.82[MKK][hapmap]
rs3735613	0.80[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs62483580	0.92[ASN][1000 genomes]
rs62483581	0.92[ASN][1000 genomes]
rs6466157	0.92[ASN][1000 genomes]
rs6466158	0.91[ASN][1000 genomes]
rs6946733	0.91[MKK][hapmap]
rs6952920	0.91[ASN][1000 genomes]
rs6969719	0.81[JPT][hapmap]
rs717099	0.83[JPT][hapmap]
rs741008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7790497	0.91[ASN][1000 genomes]
rs7809330	0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs917760	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9648946	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

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	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3801969	PSMC2	cis	parietal	SCAN
rs3801969	HBP1	cis	parietal	SCAN
rs3801969	MLL5	cis	parietal	SCAN
rs3801969	LHFPL3	cis	parietal	SCAN
rs3801969	COG5	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106701600-106716000	Weak transcription	HUVEC	blood vessel
2	chr7:106706400-106711800	Weak transcription	Brain Anterior Caudate	brain
3	chr7:106706400-106718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:106706400-106720000	Weak transcription	Spleen	Spleen
5	chr7:106706800-106719200	Weak transcription	Fetal Brain Male	brain
6	chr7:106708800-106718600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:106710200-106720000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:106710400-106712800	Strong transcription	K562	blood
9	chr7:106711200-106711600	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr7:106711400-106716000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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