Variant report

Variant	rs1381038
Chromosome Location	chr9:6333156-6333157
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10115294	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10123132	1.00[CEU][hapmap]
rs10123605	0.96[EUR][1000 genomes]
rs10125053	1.00[CEU][hapmap]
rs10125090	1.00[CEU][hapmap]
rs10125313	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs1037885	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1048279	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];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10739104	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs10758762	1.00[EUR][1000 genomes]
rs10758763	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10758768	0.96[EUR][1000 genomes]
rs10815400	0.96[EUR][1000 genomes]
rs10815401	0.96[EUR][1000 genomes]
rs10815429	0.86[EUR][1000 genomes]
rs10815430	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs10975501	0.85[CEU][hapmap]
rs1156869	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1322170	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13283687	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13284032	1.00[GIH][hapmap]
rs13285152	0.88[EUR][1000 genomes]
rs13285458	0.88[EUR][1000 genomes]
rs13291494	0.88[EUR][1000 genomes]
rs13293015	0.83[EUR][1000 genomes]
rs13293673	0.91[EUR][1000 genomes]
rs13296481	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13298872	0.96[EUR][1000 genomes]
rs13299896	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13302032	0.88[EUR][1000 genomes]
rs1330381	0.96[EUR][1000 genomes]
rs1407357	1.00[EUR][1000 genomes]
rs1407358	1.00[EUR][1000 genomes]
rs1412420	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs16924360	0.85[MKK][hapmap];0.94[YRI][hapmap]
rs1854709	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs1855022	0.84[EUR][1000 genomes]
rs2000198	0.88[EUR][1000 genomes]
rs2019737	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2051003	0.88[EUR][1000 genomes]
rs2150964	0.81[EUR][1000 genomes]
rs2150971	0.88[EUR][1000 genomes]
rs2381438	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28615746	0.96[EUR][1000 genomes]
rs2890707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34530211	0.88[EUR][1000 genomes]
rs34581400	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35301257	0.88[EUR][1000 genomes]
rs35408061	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36089474	0.88[EUR][1000 genomes]
rs3847262	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3858051	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4008347	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs424119	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4475552	0.91[EUR][1000 genomes]
rs4742172	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs4742177	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4742180	0.96[EUR][1000 genomes]
rs4742198	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742200	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742203	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs503315	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs553048	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477060	0.88[EUR][1000 genomes]
rs6477067	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67541153	1.00[EUR][1000 genomes]
rs7021445	0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.91[EUR][1000 genomes]
rs7035574	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7036990	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7039968	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7040374	0.88[EUR][1000 genomes]
rs7041863	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs7043824	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7043887	0.96[EUR][1000 genomes]
rs7044749	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7045164	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7048431	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72693587	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7350177	0.96[EUR][1000 genomes]
rs7851921	0.96[EUR][1000 genomes]
rs7852138	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	0.91[EUR][1000 genomes]
rs7858373	1.00[EUR][1000 genomes]
rs7859139	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864212	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];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs922221	0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.96[EUR][1000 genomes]
rs980850	0.88[EUR][1000 genomes]
rs993952	0.83[AMR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1381038	C9orf38	Cis_1M	lymphoblastoid	RTeQTL
rs1381038	UHRF2	Cis_1M	lymphoblastoid	RTeQTL
rs1381038	ERMP1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6328400-6335800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links