Variant report

Variant	rs62558320
Chromosome Location	chr9:17268590-17268591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10810743	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810745	0.88[EUR][1000 genomes]
rs10810746	0.88[EUR][1000 genomes]
rs10810755	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810759	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810762	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810772	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810776	0.81[EUR][1000 genomes]
rs10962907	0.90[ASN][1000 genomes]
rs10962944	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10962949	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10962954	0.87[ASN][1000 genomes]
rs10962956	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10962958	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10962959	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10962993	0.88[EUR][1000 genomes]
rs10962994	0.88[EUR][1000 genomes]
rs10962996	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962998	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962999	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963000	0.88[EUR][1000 genomes]
rs10963001	0.87[EUR][1000 genomes]
rs10963005	0.86[EUR][1000 genomes]
rs10963015	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963017	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963018	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963019	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963022	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963025	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963030	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10963031	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963036	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963039	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963040	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963041	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10963060	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10963064	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10963065	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11515075	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11523716	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523726	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11789418	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11789741	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789786	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791000	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11791463	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11795325	0.89[EUR][1000 genomes]
rs12376505	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12376938	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376973	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377081	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377334	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12378677	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379538	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379655	0.91[EUR][1000 genomes]
rs12551355	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283891	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13286311	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287407	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289670	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13289755	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13290659	0.89[EUR][1000 genomes]
rs13292365	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13292380	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13292550	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301284	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17755748	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17828423	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829280	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953106	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027014	0.89[EUR][1000 genomes]
rs2095156	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151342	0.81[EUR][1000 genomes]
rs2184063	0.89[EUR][1000 genomes]
rs2383013	0.88[EUR][1000 genomes]
rs34189605	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34256131	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34502029	0.89[EUR][1000 genomes]
rs34597155	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34768018	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375281	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35601090	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35884270	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35968717	0.88[EUR][1000 genomes]
rs35998538	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063154	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077273	0.85[EUR][1000 genomes]
rs3739490	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808791	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808795	0.91[EUR][1000 genomes]
rs4317676	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375098	0.89[EUR][1000 genomes]
rs4405013	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574939	0.86[EUR][1000 genomes]
rs4626705	0.88[EUR][1000 genomes]
rs59833414	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60520802	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61565870	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62558297	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62558300	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62558301	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62558354	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62558966	0.81[EUR][1000 genomes]
rs7026852	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041744	0.88[EUR][1000 genomes]
rs7042230	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867175	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv892662	chr9:17168867-17329964	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1031269	chr9:17204320-17316969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv466270	chr9:17236376-17377629	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv613694	chr9:17236376-17377629	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv892663	chr9:17243746-17329964	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv892664	chr9:17250170-17296630	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv892665	chr9:17250170-17371690	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv892666	chr9:17256043-17280616	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62558320	CNTLN	cis	Nerve Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17223600-17279400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:17247400-17269000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:17260600-17269000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:17262600-17280400	Weak transcription	Liver	Liver
5	chr9:17262800-17339800	Weak transcription	Left Ventricle	heart
6	chr9:17268200-17269200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:17268400-17269000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:17268400-17269000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:17268400-17269000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr9:17268400-17269200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:17268400-17269200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr9:17268400-17269400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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