Variant report

Variant	rs4852939
Chromosome Location	chr2:73856769-73856770
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10190002	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10197233	0.90[ASN][1000 genomes]
rs1052161	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap]
rs10865398	0.83[ASW][hapmap];0.96[CEU][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap]
rs11126411	0.94[JPT][hapmap]
rs11126413	0.90[EUR][1000 genomes]
rs11126414	0.81[TSI][hapmap]
rs11126417	0.81[TSI][hapmap]
rs11683970	0.93[ASN][1000 genomes]
rs11894953	0.81[TSI][hapmap]
rs12466032	0.88[YRI][hapmap]
rs12478871	0.82[JPT][hapmap]
rs12618600	0.96[CEU][hapmap];0.92[GIH][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap]
rs12620018	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12620091	0.80[CEU][hapmap]
rs12713793	0.81[TSI][hapmap]
rs12713798	0.81[TSI][hapmap]
rs12991161	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs13007306	0.93[ASN][1000 genomes]
rs13007607	0.88[EUR][1000 genomes]
rs13009035	0.85[EUR][1000 genomes]
rs13017182	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs13018422	0.88[EUR][1000 genomes]
rs13022145	0.89[EUR][1000 genomes]
rs13027816	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1320374	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17350188	0.81[TSI][hapmap]
rs2280506	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2280507	0.84[JPT][hapmap]
rs2421574	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2421582	0.95[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421583	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421584	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421586	1.00[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421587	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2421660	0.92[ASN][1000 genomes]
rs2421661	0.88[ASN][1000 genomes]
rs2421662	0.93[ASN][1000 genomes]
rs2421667	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421668	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap]
rs2421674	0.81[TSI][hapmap]
rs2421676	0.81[TSI][hapmap]
rs2860579	0.89[ASN][1000 genomes]
rs2947845	0.90[JPT][hapmap]
rs34874205	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4241256	0.93[ASN][1000 genomes]
rs4341964	0.87[EUR][1000 genomes]
rs4346412	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4627598	0.90[JPT][hapmap]
rs4852308	0.86[EUR][1000 genomes]
rs4852309	0.93[ASN][1000 genomes]
rs4852311	0.88[JPT][hapmap]
rs4852937	0.81[ASN][1000 genomes]
rs4852940	0.97[ASN][1000 genomes]
rs4852950	0.87[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4852954	0.92[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4852959	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4852975	0.81[TSI][hapmap]
rs4852976	0.86[TSI][hapmap]
rs6546862	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6722867	0.86[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6742619	0.91[CEU][hapmap]
rs6743576	0.86[EUR][1000 genomes]
rs6744273	0.88[JPT][hapmap]
rs6745560	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs6749680	0.83[ASW][hapmap];0.84[CEU][hapmap];0.85[MKK][hapmap]
rs6755948	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6757996	0.81[EUR][1000 genomes]
rs7566315	0.84[EUR][1000 genomes]
rs7570683	1.00[CEU][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7574240	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7574268	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7579068	0.89[JPT][hapmap]
rs7598660	0.87[CEU][hapmap]
rs7598901	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap]
rs7606947	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs7607989	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs7609249	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1015036	chr2:73840055-73891004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1006235	chr2:73840055-73896603	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1006033	chr2:73840055-73900856	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv2760600	chr2:73846605-73911523	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv874271	chr2:73847024-73907696	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv874272	chr2:73847024-73914019	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv874273	chr2:73847024-73916672	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv874274	chr2:73847024-73922475	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv874275	chr2:73847024-73931971	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	nsv979021	chr2:73847283-73871861	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1013586	chr2:73848777-73906844	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv1004208	chr2:73849172-73911511	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	esv2497164	chr2:73850717-73912022	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv1004886	chr2:73852525-73900856	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1011488	chr2:73852525-73909818	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv1000057	chr2:73852525-73911511	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	esv3385057	chr2:73853505-73913858	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv1013142	chr2:73854911-73911511	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv1008311	chr2:73854911-73923089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv829460	chr2:73856145-73913711	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4852939	ALMS1	cis	brain	seeQTL
rs4852939	ALMS1P	cis	Nerve Tibial	GTEx
rs4852939	ALMS1	trans	brain	seeQTL
rs4852939	CGI-121	cis	multi-tissue	Pritchard
rs4852939	C2orf78	cis	brain	seeQTL
rs4852939	DCTN1	cis	brain	seeQTL
rs4852939	HIST1H2BE	trans	brain	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73852400-73857400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr2:73854000-73858000	Weak transcription	Liver	Liver
3	chr2:73855600-73857000	Enhancers	GM12878-XiMat	blood
4	chr2:73856600-73857000	Weak transcription	HSMMtube	muscle

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