Variant report

Variant	rs2235868
Chromosome Location	chr6:39040654-39040655
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	chr6:39032106..39033612-chr6:39039523..39041550,2	K562	blood:
2	chr6:39040219..39042267-chr6:39046191..39048280,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1042044	0.89[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1126476	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12201075	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12214482	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12214488	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2268644	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2268647	0.91[EUR][1000 genomes]
rs2300615	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2300616	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3765466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711571	0.94[ASN][1000 genomes]
rs4711572	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711573	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711575	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57248948	0.94[ASN][1000 genomes]
rs6458093	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906372	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341356	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7341358	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7341360	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765641	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765879	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7766068	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766275	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766663	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs877446	0.92[CEU][hapmap]
rs910162	0.80[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs910163	0.83[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs910165	0.94[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910170	0.88[CEU][hapmap]
rs9296277	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296278	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296279	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296281	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296282	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296283	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296284	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296287	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9357298	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394573	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv528286	chr6:39019503-39060478	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv470815	chr6:39022698-39051694	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv519907	chr6:39032415-39055012	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1031922	chr6:39034484-39060762	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1793081	chr6:39034516-39048562	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2235868	PPP2R5D	cis	cerebellum	SCAN
rs2235868	KCNK16	cis	parietal	SCAN
rs2235868	RNF8	cis	cerebellum	SCAN
rs2235868	LHFPL5	cis	cerebellum	SCAN
rs2235868	SRPK1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39021200-39072000	Weak transcription	Gastric	stomach
2	chr6:39022400-39041600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:39024200-39057800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:39027400-39073000	Weak transcription	Pancreas	Pancrea
5	chr6:39030400-39044800	Weak transcription	Right Atrium	heart
6	chr6:39033600-39052200	Weak transcription	Right Ventricle	heart
7	chr6:39034000-39042400	Weak transcription	Fetal Heart	heart
8	chr6:39036400-39050200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:39039200-39040800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:39040200-39041800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:39040200-39042000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:39040400-39043200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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