Variant report

Variant	rs4742180
Chromosome Location	chr9:6352776-6352777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10115294	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10123132	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10123605	1.00[EUR][1000 genomes]
rs10125053	1.00[CEU][hapmap]
rs10125090	1.00[CEU][hapmap]
rs10125313	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1037885	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1048279	0.92[EUR][1000 genomes]
rs10491838	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739096	1.00[EUR][1000 genomes]
rs10739101	0.96[EUR][1000 genomes]
rs10739103	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739104	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10758762	0.96[EUR][1000 genomes]
rs10758763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10758768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10815400	1.00[EUR][1000 genomes]
rs10815401	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10815429	0.91[EUR][1000 genomes]
rs10815430	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10815441	1.00[YRI][hapmap]
rs10975501	0.85[CEU][hapmap]
rs1156869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs12346381	0.84[EUR][1000 genomes]
rs1322170	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13283464	1.00[YRI][hapmap]
rs13283631	1.00[YRI][hapmap]
rs13283687	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13284032	1.00[YRI][hapmap]
rs13284392	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13285152	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13285458	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13286720	1.00[YRI][hapmap]
rs13288875	1.00[YRI][hapmap]
rs13290126	1.00[YRI][hapmap]
rs13291494	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13291887	1.00[YRI][hapmap]
rs13292030	1.00[YRI][hapmap]
rs13293015	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13293673	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13296481	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13298872	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13299896	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13300059	1.00[YRI][hapmap]
rs13302032	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1330381	1.00[EUR][1000 genomes]
rs1381038	0.96[EUR][1000 genomes]
rs1407357	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1407358	0.96[EUR][1000 genomes]
rs1412420	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs1563	1.00[YRI][hapmap]
rs16924678	1.00[YRI][hapmap]
rs16924682	1.00[YRI][hapmap]
rs1854709	0.85[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs1855022	0.88[EUR][1000 genomes]
rs2000198	0.92[EUR][1000 genomes]
rs2019737	0.96[EUR][1000 genomes]
rs2051003	0.92[EUR][1000 genomes]
rs2150964	0.85[EUR][1000 genomes]
rs2150971	0.92[EUR][1000 genomes]
rs2282158	1.00[YRI][hapmap]
rs2297443	1.00[YRI][hapmap]
rs2381438	0.87[EUR][1000 genomes]
rs28615746	1.00[EUR][1000 genomes]
rs2890707	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs34530211	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34581400	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35301257	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35408061	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36089474	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818705	1.00[YRI][hapmap]
rs3847262	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3858051	0.96[EUR][1000 genomes]
rs4008347	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs424119	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4475552	0.87[EUR][1000 genomes]
rs4742172	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4742177	0.96[EUR][1000 genomes]
rs4742198	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742200	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742203	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs503315	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs553048	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6477060	0.92[EUR][1000 genomes]
rs6477067	0.96[EUR][1000 genomes]
rs67541153	0.96[EUR][1000 genomes]
rs7021445	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031407	1.00[EUR][1000 genomes]
rs7031967	0.96[EUR][1000 genomes]
rs7032411	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7035574	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7036990	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7039968	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7040374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7041863	1.00[CEU][hapmap]
rs7043824	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7043887	1.00[EUR][1000 genomes]
rs7044749	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7045164	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7048431	0.87[EUR][1000 genomes]
rs72693587	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7350177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7851921	1.00[EUR][1000 genomes]
rs7852138	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853322	0.96[EUR][1000 genomes]
rs7858373	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7859139	0.96[EUR][1000 genomes]
rs7864212	0.96[EUR][1000 genomes]
rs7869419	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7873206	1.00[EUR][1000 genomes]
rs898673	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs922221	1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980849	1.00[EUR][1000 genomes]
rs980850	0.92[EUR][1000 genomes]
rs993952	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv1019222	chr9:6328242-6402856	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4742180	UHRF2	Cis_1M	lymphoblastoid	RTeQTL
rs4742180	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6351000-6355800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:6351400-6352800	Enhancers	Hela-S3	cervix
3	chr9:6352200-6353800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:6352200-6354000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:6352400-6354000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:6352400-6354400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:6352600-6353000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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