Variant report

Variant	rs6759452
Chromosome Location	chr2:73878352-73878353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73878117..73880708-chr2:73881565..73884435,2	K562	blood:

Extended variants
information (count: 150 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10168931	1.00[ASN][1000 genomes]
rs10169213	1.00[ASN][1000 genomes]
rs10169714	1.00[ASN][1000 genomes]
rs10173534	1.00[ASN][1000 genomes]
rs10178678	1.00[ASN][1000 genomes]
rs10181563	1.00[ASN][1000 genomes]
rs10183818	1.00[ASN][1000 genomes]
rs10185080	1.00[ASN][1000 genomes]
rs10187192	1.00[ASN][1000 genomes]
rs10193972	0.82[CEU][hapmap]
rs10197755	1.00[ASN][1000 genomes]
rs10198549	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs10199224	1.00[ASN][1000 genomes]
rs10206899	0.89[CEU][hapmap]
rs10207220	1.00[ASN][1000 genomes]
rs10469966	1.00[ASN][1000 genomes]
rs10496192	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	0.82[CEU][hapmap]
rs1114380	1.00[ASN][1000 genomes]
rs11674602	1.00[ASN][1000 genomes]
rs11675958	1.00[ASN][1000 genomes]
rs11676385	1.00[ASN][1000 genomes]
rs11679042	0.88[EUR][1000 genomes]
rs11679594	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680965	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11686541	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11689164	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689588	1.00[ASN][1000 genomes]
rs11693586	1.00[ASN][1000 genomes]
rs11693588	1.00[ASN][1000 genomes]
rs11884776	1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11893881	1.00[ASN][1000 genomes]
rs11901272	0.82[CEU][hapmap]
rs13384756	1.00[ASN][1000 genomes]
rs13384952	1.00[ASN][1000 genomes]
rs13385564	1.00[ASN][1000 genomes]
rs13391552	1.00[ASN][1000 genomes]
rs13392691	1.00[ASN][1000 genomes]
rs13392872	1.00[ASN][1000 genomes]
rs13398956	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13400985	1.00[ASN][1000 genomes]
rs13409366	1.00[ASN][1000 genomes]
rs13410232	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13421462	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13431267	1.00[ASN][1000 genomes]
rs13431529	1.00[ASN][1000 genomes]
rs13432605	1.00[ASN][1000 genomes]
rs13538	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs1403284	1.00[ASN][1000 genomes]
rs1589576	1.00[ASN][1000 genomes]
rs17009149	1.00[ASN][1000 genomes]
rs17009159	1.00[ASN][1000 genomes]
rs2056486	0.82[CEU][hapmap]
rs2421552	1.00[ASN][1000 genomes]
rs2567598	1.00[ASN][1000 genomes]
rs2567601	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2567602	1.00[ASN][1000 genomes]
rs2567603	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28879089	1.00[ASN][1000 genomes]
rs4547554	1.00[ASN][1000 genomes]
rs56131703	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56154726	1.00[ASN][1000 genomes]
rs62149774	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149777	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149781	1.00[ASN][1000 genomes]
rs62149782	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62149804	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62151646	1.00[ASN][1000 genomes]
rs62151652	1.00[ASN][1000 genomes]
rs62153182	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62153183	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	0.82[CEU][hapmap]
rs6546839	0.82[CEU][hapmap]
rs6546854	1.00[ASN][1000 genomes]
rs6546857	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6546858	0.88[CEU][hapmap]
rs6704782	1.00[ASN][1000 genomes]
rs6708766	1.00[ASN][1000 genomes]
rs6710438	1.00[ASN][1000 genomes]
rs6711033	0.89[CEU][hapmap]
rs6724782	0.82[CEU][hapmap]
rs6735946	1.00[ASN][1000 genomes]
rs6740766	1.00[ASN][1000 genomes]
rs6744398	1.00[ASN][1000 genomes]
rs6745368	1.00[ASN][1000 genomes]
rs6745480	0.89[CEU][hapmap]
rs6756885	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs6756987	0.82[CEU][hapmap]
rs73947808	1.00[ASN][1000 genomes]
rs7424690	1.00[ASN][1000 genomes]
rs7558944	1.00[ASN][1000 genomes]
rs7572722	1.00[ASN][1000 genomes]
rs7582051	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582606	1.00[ASN][1000 genomes]
rs7583255	1.00[ASN][1000 genomes]
rs7586463	1.00[ASN][1000 genomes]
rs7587577	1.00[ASN][1000 genomes]
rs7594511	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7596773	1.00[ASN][1000 genomes]
rs7602980	1.00[ASN][1000 genomes]
rs7603647	1.00[ASN][1000 genomes]
rs7607892	1.00[ASN][1000 genomes]
rs9309473	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9653557	1.00[ASN][1000 genomes]
rs9750915	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:45 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	nsv582209	chr2:73857002-73907696	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking 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
29	nsv818044	chr2:73859184-73906819	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv515605	chr2:73859184-73916672	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
31	esv3334222	chr2:73867401-73923991	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	nsv874277	chr2:73870010-73931971	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	nsv874278	chr2:73870010-73931971	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	esv3340115	chr2:73870416-73930142	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
35	nsv582210	chr2:73870573-73916672	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
36	nsv874279	chr2:73870573-73916672	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
37	nsv874280	chr2:73870573-73927764	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
38	esv2762675	chr2:73875799-73928886	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
39	nsv441760	chr2:73875799-73928886	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
40	esv3426494	chr2:73876125-73939153	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
41	nsv979335	chr2:73876316-73897805	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
42	esv3460808	chr2:73877074-73940302	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
43	esv3460809	chr2:73877074-73940302	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
44	nsv829461	chr2:73877427-73931225	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
45	nsv874281	chr2:73878352-73927764	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6759452	ALMS1P	cis	cerebellum	SCAN
rs6759452	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6759452	ALMS1P	cis	Thyroid	GTEx
rs6759452	ALMS1	cis	cerebellum	SCAN
rs6759452	ALMS1	cis	normal skin	skin_eQTL
rs6759452	ALMS1P	cis	Stomach	GTEx
rs6759452	EXOC6B	cis	cerebellum	SCAN
rs6759452	ALMS1	cis	multi-tissue	Pritchard
rs6759452	ALMS1	cis	parietal	SCAN
rs6759452	ALMS1P	cis	parietal	SCAN
rs6759452	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6759452	ALMS1P	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73871200-73878800	Weak transcription	Liver	Liver
2	chr2:73876000-73880800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:73877800-73878600	Enhancers	Fetal Lung	lung
4	chr2:73878200-73878800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr2:73878200-73879200	Enhancers	GM12878-XiMat	blood

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