Variant report

Variant	rs6744398
Chromosome Location	chr2:73897144-73897145
allele	A/G
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	FOXA1	chr2:73897026-73897600	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:73897038-73897597	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ALMS1P	TF binding region

Extended variants
information (count: 143 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10168931	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169213	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10169714	1.00[ASN][1000 genomes]
rs10173534	1.00[ASN][1000 genomes]
rs10178409	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10178678	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10181563	1.00[ASN][1000 genomes]
rs10183818	1.00[ASN][1000 genomes]
rs10185080	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	1.00[ASN][1000 genomes]
rs10197755	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10199224	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10206899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207220	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10469966	1.00[ASN][1000 genomes]
rs1114380	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	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11893881	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384756	0.90[AMR][1000 genomes];0.98[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	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	1.00[ASN][1000 genomes]
rs13392872	1.00[ASN][1000 genomes]
rs13398956	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13400985	1.00[ASN][1000 genomes]
rs13409366	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421462	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13431267	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13431529	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432605	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13538	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403284	1.00[ASN][1000 genomes]
rs1589576	1.00[ASN][1000 genomes]
rs17009149	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17009159	1.00[ASN][1000 genomes]
rs2421552	0.81[AMR][1000 genomes];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	0.93[AFR][1000 genomes]
rs28879089	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4547554	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[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	0.81[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]
rs6546854	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.84[EUR][1000 genomes]
rs6704782	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6705977	0.84[EUR][1000 genomes]
rs6708766	1.00[ASN][1000 genomes]
rs6710438	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6711001	0.85[EUR][1000 genomes]
rs6718843	0.84[EUR][1000 genomes]
rs6735946	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6745368	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	1.00[ASN][1000 genomes]
rs6759452	1.00[ASN][1000 genomes]
rs73947808	1.00[ASN][1000 genomes]
rs7424690	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7558944	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7582051	1.00[ASN][1000 genomes]
rs7582606	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7583255	1.00[ASN][1000 genomes]
rs7586463	1.00[ASN][1000 genomes]
rs7587577	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596773	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	1.00[ASN][1000 genomes]
rs7603647	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	1.00[ASN][1000 genomes]
rs9309473	0.82[AMR][1000 genomes]
rs9653557	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:46 , 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	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	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
38	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
39	nsv979335	chr2:73876316-73897805	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
40	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
41	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
42	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
43	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
44	nsv874282	chr2:73878827-73922475	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
45	nsv874283	chr2:73878827-73927764	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
46	esv2753082	chr2:73891045-73955545	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6744398	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6744398	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6744398	ALMS1P	cis	Nerve Tibial	GTEx
rs6744398	ALMS1P	cis	Thyroid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73896200-73905200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:73896800-73897800	Enhancers	HepG2	liver
3	chr2:73897000-73897200	Enhancers	Gastric	stomach

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