Variant report

Variant	rs13538
Chromosome Location	chr2:73868328-73868329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr2:73868230-73868420	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALMS1-2	chr2:73868076-73868755	NONHSAT071625

Variant related genes	Relation type
ALMS1P	TF binding region

Extended variants
information (count: 146 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10168931	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169213	1.00[ASN][1000 genomes]
rs10169714	1.00[ASN][1000 genomes]
rs10173534	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10178409	0.89[AMR][1000 genomes];0.90[EUR][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]
rs10190219	1.00[ASN][1000 genomes]
rs10193972	0.94[CEU][hapmap]
rs10197755	1.00[ASN][1000 genomes]
rs10198549	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10199224	1.00[ASN][1000 genomes]
rs10206899	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10207220	1.00[ASN][1000 genomes]
rs10469966	1.00[ASN][1000 genomes]
rs10496192	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs1052162	0.94[CEU][hapmap]
rs1114380	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11674602	1.00[ASN][1000 genomes]
rs11675958	1.00[ASN][1000 genomes]
rs11676385	1.00[ASN][1000 genomes]
rs11679594	1.00[ASN][1000 genomes]
rs11680965	1.00[ASN][1000 genomes]
rs11686541	1.00[ASN][1000 genomes]
rs11689164	1.00[ASN][1000 genomes]
rs11689588	1.00[ASN][1000 genomes]
rs11693586	1.00[ASN][1000 genomes]
rs11693588	1.00[ASN][1000 genomes]
rs11884776	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs11893881	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901272	0.94[CEU][hapmap]
rs13384756	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	1.00[ASN][1000 genomes]
rs13385564	1.00[ASN][1000 genomes]
rs13391258	0.84[EUR][1000 genomes]
rs13391552	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	1.00[ASN][1000 genomes]
rs13392872	1.00[ASN][1000 genomes]
rs13398956	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs13400985	1.00[ASN][1000 genomes]
rs13409366	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421462	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs13431267	1.00[ASN][1000 genomes]
rs13431529	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432605	0.82[AMR][1000 genomes];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	0.94[CEU][hapmap]
rs2421552	1.00[ASN][1000 genomes]
rs2567598	1.00[ASN][1000 genomes]
rs2567601	1.00[ASN][1000 genomes]
rs2567602	1.00[ASN][1000 genomes]
rs2567603	1.00[ASN][1000 genomes]
rs28525015	0.83[AFR][1000 genomes]
rs28879089	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4547554	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56154726	1.00[ASN][1000 genomes]
rs62149774	1.00[ASN][1000 genomes]
rs62149777	1.00[ASN][1000 genomes]
rs62149781	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62149782	1.00[ASN][1000 genomes]
rs62149804	1.00[ASN][1000 genomes]
rs62151646	1.00[ASN][1000 genomes]
rs62151652	1.00[ASN][1000 genomes]
rs62153182	1.00[ASN][1000 genomes]
rs62153183	1.00[ASN][1000 genomes]
rs6546836	0.83[CEU][hapmap]
rs6546837	0.94[CEU][hapmap]
rs6546838	0.94[CEU][hapmap]
rs6546839	0.94[CEU][hapmap]
rs6546854	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6546858	1.00[CEU][hapmap]
rs6546861	0.84[EUR][1000 genomes]
rs6704782	1.00[ASN][1000 genomes]
rs6705977	0.84[EUR][1000 genomes]
rs6708766	1.00[ASN][1000 genomes]
rs6710438	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6711001	0.85[EUR][1000 genomes]
rs6711033	1.00[CEU][hapmap]
rs6718843	0.84[EUR][1000 genomes]
rs6724782	0.94[CEU][hapmap]
rs6735946	1.00[ASN][1000 genomes]
rs6736866	1.00[ASN][1000 genomes]
rs6740766	1.00[ASN][1000 genomes]
rs6744398	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745368	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6745480	1.00[CEU][hapmap]
rs6756885	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6756987	0.94[CEU][hapmap]
rs6759452	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs73947808	1.00[ASN][1000 genomes]
rs7424690	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7558944	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	1.00[ASN][1000 genomes]
rs7582051	1.00[ASN][1000 genomes]
rs7582606	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7583255	1.00[ASN][1000 genomes]
rs7586463	1.00[ASN][1000 genomes]
rs7587577	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7596773	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	1.00[ASN][1000 genomes]
rs7603647	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs9653557	1.00[ASN][1000 genomes]
rs9750915	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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

Variant related diseases (count:5)

Disease	PMID	Source
Blood metabolite ratios	24816252	GWAS catalog
Blood metabolite levels	24816252	GWAS catalog
Metabolite levels (X-11787)	23934736	GWAS catalog
Serum metabolite levels	24625756	GWAS catalog
Chronic kidney disease	20383146	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13538	ALMS1P	cis	Nerve Tibial	GTEx
rs13538	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs13538	ALMS1P	cis	Thyroid	GTEx
rs13538	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs13538	ALMS1	cis	normal skin	skin_eQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73866200-73870600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:73866400-73868800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:73866400-73871200	Enhancers	Fetal Lung	lung
4	chr2:73867000-73868600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr2:73867000-73872200	Enhancers	Ovary	ovary
6	chr2:73867200-73869000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr2:73867200-73869800	Enhancers	Colonic Mucosa	Colon
8	chr2:73867400-73868400	Enhancers	Brain Hippocampus Middle	brain
9	chr2:73867400-73868600	Enhancers	Adipose Nuclei	Adipose
10	chr2:73867400-73868600	Enhancers	Brain Cingulate Gyrus	brain
11	chr2:73867400-73869800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:73867400-73870200	Flanking Active TSS	Liver	Liver
13	chr2:73867400-73870200	Enhancers	Fetal Intestine Large	intestine
14	chr2:73867600-73868400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:73867600-73868400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:73867600-73868400	Enhancers	Pancreas	Pancrea
17	chr2:73867600-73868600	Enhancers	Brain Angular Gyrus	brain
18	chr2:73867600-73868600	Enhancers	Brain Substantia Nigra	brain
19	chr2:73867600-73868600	Enhancers	Lung	lung
20	chr2:73867600-73868600	Enhancers	Stomach Mucosa	stomach
21	chr2:73867600-73872200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:73867800-73868400	Enhancers	Spleen	Spleen
23	chr2:73867800-73868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:73867800-73870000	Enhancers	Placenta	Placenta
25	chr2:73868000-73868600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr2:73868000-73868600	Enhancers	Gastric	stomach
27	chr2:73868000-73868800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:73868000-73869000	Flanking Bivalent TSS/Enh	HepG2	liver
29	chr2:73868000-73869200	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:73868200-73868400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:73868200-73868400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:73868200-73868400	Enhancers	Left Ventricle	heart
33	chr2:73868200-73868600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr2:73868200-73869800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:73868200-73870000	Enhancers	Fetal Intestine Small	intestine

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