Variant report

Variant	rs5009239
Chromosome Location	chr7:119235561-119235562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:119090628..119092465-chr7:119234986..119236766,2	K562	blood:
2	chr7:119234213..119235745-chr7:119237438..119239172,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10239992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10245797	0.88[ASN][1000 genomes]
rs10246845	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10251920	0.84[ASN][1000 genomes]
rs10258423	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10266505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10267600	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10267793	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10271355	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10274141	0.88[ASN][1000 genomes]
rs10275167	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10279364	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10500075	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11767407	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11770085	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11771830	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11973192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12537312	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12540739	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12706258	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1404083	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs17279575	0.82[AFR][1000 genomes]
rs17345578	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs28843793	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28893249	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4129182	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs4132827	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4341091	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4486113	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4518596	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4617096	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4727897	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4727901	0.88[ASN][1000 genomes]
rs4730924	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730929	0.84[ASN][1000 genomes]
rs4730930	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4730933	0.88[ASN][1000 genomes]
rs4730935	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs58141692	0.88[ASN][1000 genomes]
rs58374970	0.82[AFR][1000 genomes]
rs62477384	0.84[ASN][1000 genomes]
rs6466707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6466708	0.88[ASN][1000 genomes]
rs6466714	0.82[AFR][1000 genomes]
rs6943195	0.81[ASN][1000 genomes]
rs6946759	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6948585	0.82[AFR][1000 genomes]
rs6955486	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6955609	0.84[ASN][1000 genomes]
rs6958096	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73483305	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73483374	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73719952	0.80[EUR][1000 genomes]
rs73720503	0.88[ASN][1000 genomes]
rs73722420	0.88[ASN][1000 genomes]
rs73722422	0.88[ASN][1000 genomes]
rs73722423	0.88[ASN][1000 genomes]
rs7777009	0.84[ASN][1000 genomes]
rs7778068	0.83[ASN][1000 genomes]
rs7782632	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7796017	0.88[ASN][1000 genomes]
rs7799128	0.88[ASN][1000 genomes]
rs7799153	0.88[ASN][1000 genomes]
rs7799166	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889100	chr7:118744450-119247571	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv949327	chr7:119179990-119402882	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv889114	chr7:119206096-119440159	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3478059	chr7:119228052-119236067	Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
5	esv3478060	chr7:119228068-119236064	Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
6	esv11548	chr7:119232822-119236164	Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv1020551	chr7:119232910-119292763	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv981410	chr7:119233323-119236164	Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv970422	chr7:119233323-119244802	Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5009239	GPR84	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:119233800-119235800	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr7:119234000-119235600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr7:119234000-119235600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr7:119234000-119236400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:119234200-119235600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr7:119234600-119235600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr7:119234600-119235800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:119234600-119235800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr7:119234600-119235800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr7:119234600-119236200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:119234800-119236400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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