Variant report

Variant	rs13340341
Chromosome Location	chr5:45860936-45860937
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	chr17:56742322..56745282-chr5:45859385..45861280,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199426	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10052736	0.88[ASN][1000 genomes]
rs10056175	0.82[EUR][1000 genomes]
rs10062325	0.80[EUR][1000 genomes]
rs10062508	0.81[EUR][1000 genomes]
rs10213756	0.86[EUR][1000 genomes]
rs28573085	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34501453	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35648163	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4276421	0.89[EUR][1000 genomes]
rs4490592	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4492125	0.80[EUR][1000 genomes]
rs4501347	0.80[EUR][1000 genomes]
rs4502836	0.80[EUR][1000 genomes]
rs6451831	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6451838	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6451841	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6451843	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6862657	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71618219	0.87[EUR][1000 genomes]
rs7443410	0.81[EUR][1000 genomes]
rs7444405	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7446649	0.90[ASN][1000 genomes]
rs7709131	0.81[EUR][1000 genomes]
rs7723218	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7727331	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[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	nsv532804	chr5:45184041-45972996	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1019807	chr5:45264656-45872829	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv537745	chr5:45264656-45872829	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916152	chr5:45273586-46115086	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1015472	chr5:45320236-45900598	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv462133	chr5:45325915-46287112	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv597980	chr5:45325915-46287112	Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1023516	chr5:45396769-45872829	Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv537748	chr5:45396769-45872829	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv462136	chr5:45406321-46228333	Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv597984	chr5:45406321-46228333	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv533064	chr5:45414583-46115086	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1031470	chr5:45472913-45872829	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv537749	chr5:45472913-45872829	Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv525575	chr5:45479425-45912967	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1034156	chr5:45482635-46224012	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1027861	chr5:45499842-46251306	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1021254	chr5:45500335-45872968	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv537750	chr5:45500335-45872968	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv530229	chr5:45506336-46115086	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv597993	chr5:45537299-46265302	Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv533265	chr5:45566963-45872828	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv597995	chr5:45666146-45996902	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv597996	chr5:45669038-46287112	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv1027084	chr5:45675353-46389261	ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv427718	chr5:45713018-45896090	Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv1033475	chr5:45771908-46250672	ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv1017290	chr5:45799447-46250672	ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	nsv537756	chr5:45799447-46250672	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv482744	chr5:45804703-45985047	Enhancers ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
31	nsv916058	chr5:45812550-46115173	ZNF genes & repeats Enhancers Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
32	nsv1031477	chr5:45812775-46160642	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
33	nsv1024533	chr5:45840303-46389261	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	nsv830284	chr5:45847975-45949310	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
35	nsv597999	chr5:45854627-46287112	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
36	nsv916433	chr5:45855174-46115173	ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
37	nsv462138	chr5:45857129-46287112	ZNF genes & repeats Enhancers Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
38	nsv598000	chr5:45857129-46287112	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
39	nsv915969	chr5:45858776-45880744	Inactive region	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
40	nsv534638	chr5:45858833-45880709	Inactive region	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
41	nsv517551	chr5:45858842-45876678	Inactive region	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
42	nsv598001	chr5:45858842-46287112	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
43	nsv1015811	chr5:45860010-46097753	ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
44	nsv1034928	chr5:45860010-46224012	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
45	esv2763929	chr5:45860022-45880382	Inactive region	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13340341	LOC647121	Cis_chr	lymphoblastoid	RTeQTL
rs13340341	EMB	cis	parietal	SCAN
rs13340341	PARP8	Cis_chr	lymphoblastoid	RTeQTL
rs13340341	MRPS30	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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