Variant report

Variant	rs2412664
Chromosome Location	chr4:56457387-56457388
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10000512	0.83[EUR][1000 genomes]
rs10011801	0.83[EUR][1000 genomes]
rs10012559	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10017749	0.80[EUR][1000 genomes]
rs10018932	0.83[EUR][1000 genomes]
rs10026315	0.81[EUR][1000 genomes]
rs1021306	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs1021307	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs10462028	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap]
rs10462033	0.87[ASN][1000 genomes]
rs1048004	0.89[ASW][hapmap];0.93[MKK][hapmap]
rs10866424	0.86[ASN][1000 genomes]
rs11240	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap]
rs11732481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[ASN][1000 genomes]
rs11732723	0.87[JPT][hapmap]
rs11932595	1.00[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs11939971	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11943456	0.87[JPT][hapmap]
rs12505265	0.87[ASN][1000 genomes]
rs12509047	0.87[ASN][1000 genomes]
rs13133077	0.93[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs13134079	0.87[ASN][1000 genomes]
rs13434995	0.83[EUR][1000 genomes]
rs1488941	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1522109	0.87[ASN][1000 genomes]
rs1546004	0.87[ASN][1000 genomes]
rs17721497	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs17722870	0.84[ASN][1000 genomes]
rs17722979	0.89[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs17725110	0.82[EUR][1000 genomes]
rs17725163	0.81[EUR][1000 genomes]
rs17776975	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs17779627	0.84[ASN][1000 genomes]
rs17781708	0.81[EUR][1000 genomes]
rs1801260	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap]
rs1873090	0.82[EUR][1000 genomes]
rs1873091	0.82[EUR][1000 genomes]
rs1967078	0.91[ASN][1000 genomes]
rs1979604	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1979605	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2070062	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs2101476	1.00[ASN][1000 genomes]
rs2130038	1.00[ASN][1000 genomes]
rs2130040	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs2412658	1.00[ASN][1000 genomes]
rs2412659	1.00[ASN][1000 genomes]
rs2412661	1.00[ASN][1000 genomes]
rs2412662	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2412666	0.82[EUR][1000 genomes]
rs28416150	0.80[EUR][1000 genomes]
rs28473211	0.81[EUR][1000 genomes]
rs28713371	0.83[EUR][1000 genomes]
rs28756087	0.83[EUR][1000 genomes]
rs2899038	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34299771	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792603	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap]
rs3805156	0.87[ASN][1000 genomes]
rs3805388	0.81[EUR][1000 genomes]
rs41324951	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs4336288	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs483978	0.89[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs4865006	0.87[ASN][1000 genomes]
rs4865012	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs4865014	0.86[ASN][1000 genomes]
rs550144	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.85[MKK][hapmap]
rs55729020	0.87[ASN][1000 genomes]
rs55849318	0.81[EUR][1000 genomes]
rs55869433	0.87[ASN][1000 genomes]
rs55885973	0.84[ASN][1000 genomes]
rs56056791	0.81[ASN][1000 genomes]
rs56152424	1.00[ASN][1000 genomes]
rs56196624	0.87[ASN][1000 genomes]
rs56288855	0.83[EUR][1000 genomes]
rs57178140	0.80[EUR][1000 genomes]
rs57338268	0.84[ASN][1000 genomes]
rs57826934	0.81[ASN][1000 genomes]
rs58476959	0.87[ASN][1000 genomes]
rs62303711	0.81[ASN][1000 genomes]
rs62303712	0.81[ASN][1000 genomes]
rs62303713	0.81[ASN][1000 genomes]
rs62303715	0.84[ASN][1000 genomes]
rs62303716	0.84[ASN][1000 genomes]
rs62303718	0.84[ASN][1000 genomes]
rs62303722	0.84[ASN][1000 genomes]
rs62303724	0.84[ASN][1000 genomes]
rs62303726	0.87[ASN][1000 genomes]
rs62303728	0.87[ASN][1000 genomes]
rs62303730	0.87[ASN][1000 genomes]
rs62303731	0.87[ASN][1000 genomes]
rs62303732	0.87[ASN][1000 genomes]
rs62305264	0.87[ASN][1000 genomes]
rs62305265	0.87[ASN][1000 genomes]
rs62305266	0.86[ASN][1000 genomes]
rs62305267	0.87[ASN][1000 genomes]
rs62305268	0.87[ASN][1000 genomes]
rs62305269	0.87[ASN][1000 genomes]
rs62305270	0.87[ASN][1000 genomes]
rs62305271	0.87[ASN][1000 genomes]
rs62308667	0.80[EUR][1000 genomes]
rs62309728	0.87[ASN][1000 genomes]
rs62309729	0.87[ASN][1000 genomes]
rs62309730	0.87[ASN][1000 genomes]
rs62309758	0.86[ASN][1000 genomes]
rs62309759	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62310862	1.00[ASN][1000 genomes]
rs62310866	1.00[ASN][1000 genomes]
rs62310884	0.81[ASN][1000 genomes]
rs6554282	0.87[ASN][1000 genomes]
rs6554283	0.87[ASN][1000 genomes]
rs6554285	0.87[ASN][1000 genomes]
rs6554290	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs6554291	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs67963898	0.84[ASN][1000 genomes]
rs6802	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6828474	0.84[ASN][1000 genomes]
rs6830728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs6842960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6846764	0.86[ASN][1000 genomes]
rs6848755	1.00[ASN][1000 genomes]
rs6851971	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs6853506	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs6858749	0.87[JPT][hapmap]
rs693367	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs716806	1.00[ASN][1000 genomes]
rs73236149	0.87[ASN][1000 genomes]
rs73236153	1.00[ASN][1000 genomes]
rs73236165	0.80[EUR][1000 genomes]
rs7659095	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs7660668	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs7665286	1.00[ASN][1000 genomes]
rs7665846	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs7681414	0.87[ASN][1000 genomes]
rs7683997	1.00[ASN][1000 genomes]
rs7697067	0.87[ASN][1000 genomes]
rs7698022	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs880358	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs972446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs9790448	0.81[ASN][1000 genomes]
rs9993599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2412664	TMEM165	cis	parietal	SCAN
rs2412664	TMEM165	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56441200-56464400	Weak transcription	K562	blood
2	chr4:56456200-56458400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links