Variant report

Variant	rs1042044
Chromosome Location	chr6:39041502-39041503
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39032106..39033612-chr6:39039523..39041550,2	K562	blood:
2	chr6:39040219..39042267-chr6:39046191..39048280,2	K562	blood:
3	chr6:39035659..39037472-chr6:39041322..39043034,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1076733	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1126476	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs12201075	0.82[EUR][1000 genomes]
rs12214482	0.82[JPT][hapmap]
rs12214488	0.82[EUR][1000 genomes]
rs2235868	0.89[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2254336	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2268644	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300616	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3765466	0.85[CEU][hapmap]
rs4711572	0.82[EUR][1000 genomes]
rs4711573	0.83[EUR][1000 genomes]
rs4711575	0.83[EUR][1000 genomes]
rs6458093	0.84[EUR][1000 genomes]
rs6906372	0.84[EUR][1000 genomes]
rs7341356	0.82[EUR][1000 genomes]
rs7341358	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs7341360	0.82[EUR][1000 genomes]
rs7765641	0.82[EUR][1000 genomes]
rs7765879	0.82[EUR][1000 genomes]
rs7766068	0.82[EUR][1000 genomes]
rs7766228	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7766275	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs877446	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs910162	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910163	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910170	0.85[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9296277	0.82[EUR][1000 genomes]
rs9296278	0.82[EUR][1000 genomes]
rs9296279	0.82[EUR][1000 genomes]
rs9296281	0.81[EUR][1000 genomes]
rs9296282	0.82[EUR][1000 genomes]
rs9296283	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9296284	0.82[EUR][1000 genomes]
rs9296287	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296288	0.85[CEU][hapmap]
rs932443	0.91[CHB][hapmap]
rs9357298	0.83[CEU][hapmap];0.82[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1042044	RNF8	cis	cerebellum	SCAN
rs1042044	KCNK16	cis	parietal	SCAN
rs1042044	PPP2R5D	cis	cerebellum	SCAN
rs1042044	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	chr6:39040200-39041800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:39040200-39042000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:39040400-39043200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:39040800-39043800	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links