Variant report

Variant	rs7039968
Chromosome Location	chr9:6326094-6326095
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10115294	0.96[EUR][1000 genomes]
rs10123605	0.96[EUR][1000 genomes]
rs10125313	0.96[EUR][1000 genomes]
rs1037885	1.00[EUR][1000 genomes]
rs1048279	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10491838	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10739096	0.96[EUR][1000 genomes]
rs10739101	0.91[EUR][1000 genomes]
rs10739103	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10739104	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10758762	1.00[EUR][1000 genomes]
rs10758763	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10758768	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815400	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815401	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815429	0.86[EUR][1000 genomes]
rs10815430	0.96[EUR][1000 genomes]
rs1156869	0.91[EUR][1000 genomes]
rs1322170	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13283687	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13284392	0.93[AMR][1000 genomes]
rs13285152	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13285458	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13291494	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13293015	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13293673	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13296481	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13298872	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299896	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13302032	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1330381	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1381038	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1407357	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1407358	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412420	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1854709	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1855022	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2000198	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2019737	1.00[EUR][1000 genomes]
rs2051003	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2150964	0.81[EUR][1000 genomes]
rs2150971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2381438	0.91[EUR][1000 genomes]
rs28615746	0.96[EUR][1000 genomes]
rs2890707	1.00[EUR][1000 genomes]
rs34530211	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34581400	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35301257	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35408061	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36089474	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3847262	1.00[EUR][1000 genomes]
rs3858051	1.00[EUR][1000 genomes]
rs4008347	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs424119	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4475552	0.91[EUR][1000 genomes]
rs4742172	0.96[EUR][1000 genomes]
rs4742177	1.00[EUR][1000 genomes]
rs4742180	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742198	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742200	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742203	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs503315	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs553048	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477060	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477067	1.00[EUR][1000 genomes]
rs67541153	1.00[EUR][1000 genomes]
rs7021445	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.91[EUR][1000 genomes]
rs7032411	0.93[AMR][1000 genomes]
rs7035574	0.88[EUR][1000 genomes]
rs7036990	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7040374	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7043824	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7043887	0.96[EUR][1000 genomes]
rs7044749	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7048431	0.91[EUR][1000 genomes]
rs72693587	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7350177	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851921	0.96[EUR][1000 genomes]
rs7852138	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7858373	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7859139	1.00[EUR][1000 genomes]
rs7864212	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869419	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7873206	0.96[EUR][1000 genomes]
rs898673	1.00[EUR][1000 genomes]
rs922221	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980850	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs993952	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
6	nsv1027270	chr9:6152434-6328227	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539968	chr9:6152434-6328227	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
11	nsv1024324	chr9:6308178-6408875	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7039968	C9orf38	Cis_1M	lymphoblastoid	RTeQTL
rs7039968	UHRF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6325400-6326200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:6326000-6326400	Enhancers	GM12878-XiMat	blood

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