Variant report

Variant	rs1407357
Chromosome Location	chr9:6302126-6302127
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10115294	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10123132	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10123605	0.96[EUR][1000 genomes]
rs10125053	1.00[CEU][hapmap]
rs10125090	1.00[CEU][hapmap]
rs10125313	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1037885	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1048279	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10491838	0.91[EUR][1000 genomes]
rs10739096	0.96[EUR][1000 genomes]
rs10739101	0.91[EUR][1000 genomes]
rs10739103	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10739104	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs10758756	0.87[AMR][1000 genomes]
rs10758762	1.00[EUR][1000 genomes]
rs10758763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10758768	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10815400	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815429	0.86[EUR][1000 genomes]
rs10815430	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10975501	0.85[CEU][hapmap]
rs1156869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs1322170	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13283464	1.00[YRI][hapmap]
rs13283631	1.00[YRI][hapmap]
rs13283687	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs13284032	1.00[YRI][hapmap]
rs13285152	0.88[EUR][1000 genomes]
rs13285458	0.88[EUR][1000 genomes]
rs13286720	1.00[YRI][hapmap]
rs13288875	1.00[YRI][hapmap]
rs13290126	1.00[YRI][hapmap]
rs13291494	0.88[EUR][1000 genomes]
rs13291887	1.00[YRI][hapmap]
rs13292030	1.00[YRI][hapmap]
rs13293015	0.83[EUR][1000 genomes]
rs13293673	0.91[EUR][1000 genomes]
rs13296481	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13298872	0.96[EUR][1000 genomes]
rs13299896	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13300059	1.00[YRI][hapmap]
rs13302032	0.88[EUR][1000 genomes]
rs1330381	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1381038	1.00[EUR][1000 genomes]
rs1407358	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1412420	0.85[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1563	1.00[YRI][hapmap]
rs1854709	0.85[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1855022	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2000198	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2019737	1.00[EUR][1000 genomes]
rs2051003	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2150964	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2150971	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2381438	0.91[EUR][1000 genomes]
rs28615746	0.96[EUR][1000 genomes]
rs2890707	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs34530211	0.88[EUR][1000 genomes]
rs34581400	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35301257	0.88[EUR][1000 genomes]
rs35408061	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36089474	0.88[EUR][1000 genomes]
rs3847262	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3858051	1.00[EUR][1000 genomes]
rs4008347	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs424119	0.91[EUR][1000 genomes]
rs4475552	0.91[EUR][1000 genomes]
rs4742172	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742177	1.00[EUR][1000 genomes]
rs4742180	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4742198	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742200	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs503315	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs553048	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477060	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477067	1.00[EUR][1000 genomes]
rs67541153	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7020305	0.82[AMR][1000 genomes]
rs7021445	0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.91[EUR][1000 genomes]
rs7035574	0.88[EUR][1000 genomes]
rs7036990	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7039968	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7040374	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7041863	1.00[CEU][hapmap]
rs7043824	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7043887	0.96[EUR][1000 genomes]
rs7044749	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7045164	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7048431	0.91[EUR][1000 genomes]
rs72693587	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7350177	0.96[EUR][1000 genomes]
rs7851921	0.96[EUR][1000 genomes]
rs7852138	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7858373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7859139	1.00[EUR][1000 genomes]
rs7864212	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869419	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7873206	0.96[EUR][1000 genomes]
rs898673	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs922221	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980850	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs993952	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	esv1823729	chr9:6301157-6308178	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1407357	C9orf38	Cis_1M	lymphoblastoid	RTeQTL
rs1407357	UHRF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6301800-6302600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:6301800-6303000	Enhancers	NHEK	skin
3	chr9:6302000-6302600	Enhancers	Brain Anterior Caudate	brain
4	chr9:6302000-6302600	Enhancers	HMEC	breast
5	chr9:6302000-6302800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:6302000-6302800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:6302000-6303000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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