Variant report

Variant	rs13161905
Chromosome Location	chr5:1417212-1417213
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	NR3C1	chr5:1416414-1417224	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1402687..1404889-chr5:1416990..1419588,2	K562	blood:

Variant related genes	Relation type
SLC6A3	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10041901	1.00[ASN][1000 genomes]
rs10068558	1.00[ASN][1000 genomes]
rs1048953	0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs11133778	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133788	1.00[ASN][1000 genomes]
rs11133792	1.00[ASN][1000 genomes]
rs11564758	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738574	1.00[ASN][1000 genomes]
rs11750173	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12188277	1.00[ASN][1000 genomes]
rs12189390	1.00[ASN][1000 genomes]
rs12516758	1.00[CHD][hapmap]
rs13162394	1.00[ASN][1000 genomes]
rs13177347	1.00[ASN][1000 genomes]
rs13180439	1.00[ASN][1000 genomes]
rs2113328	1.00[ASN][1000 genomes]
rs28382221	1.00[ASN][1000 genomes]
rs28382245	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28709633	1.00[ASN][1000 genomes]
rs34070149	1.00[ASN][1000 genomes]
rs34152723	1.00[ASN][1000 genomes]
rs35344649	1.00[ASN][1000 genomes]
rs35559535	1.00[ASN][1000 genomes]
rs35561057	1.00[ASN][1000 genomes]
rs4608970	1.00[CHD][hapmap]
rs4975553	1.00[ASN][1000 genomes]
rs4975646	1.00[ASW][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap]
rs55659724	1.00[ASN][1000 genomes]
rs55779566	1.00[ASN][1000 genomes]
rs56397275	1.00[ASN][1000 genomes]
rs58453572	1.00[ASN][1000 genomes]
rs62329734	1.00[ASN][1000 genomes]
rs62329735	1.00[ASN][1000 genomes]
rs72717518	1.00[ASN][1000 genomes]
rs72717521	1.00[ASN][1000 genomes]
rs72717524	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533223	chr5:924201-1544459	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv917123	chr5:965332-1528792	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv1023100	chr5:1149132-1558039	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv537604	chr5:1149132-1558039	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv880847	chr5:1192587-1423905	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1033213	chr5:1198042-1483573	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv537605	chr5:1198042-1483573	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv880418	chr5:1286516-1473977	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv830187	chr5:1318106-1509826	Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv482682	chr5:1324469-1487909	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv881312	chr5:1376161-1429969	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv880311	chr5:1377172-1429969	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv881664	chr5:1377172-1594879	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
14	nsv880670	chr5:1381260-1435893	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv461909	chr5:1411412-1468287	Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
16	nsv596857	chr5:1411412-1468287	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
17	nsv880402	chr5:1412645-1473977	Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
18	esv3340599	chr5:1414552-1419650	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1807179	chr5:1416646-1432825	Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv1826079	chr5:1416646-1432825	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	esv1839547	chr5:1416646-1432825	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv3324247	chr5:1417052-1421450	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13161905	CLPTM1L	cis	parietal	SCAN
rs13161905	CLPTM1L	cis	cerebellum	SCAN
rs13161905	LPCAT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1415600-1418000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:1417200-1417400	Enhancers	Spleen	Spleen

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