Variant report

Variant	rs17696599
Chromosome Location	chr10:55405246-55405247
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	chr10:55405153..55407581-chr5:63345532..63348450,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11003684	0.84[EUR][1000 genomes]
rs11003685	0.94[EUR][1000 genomes]
rs11003692	0.93[EUR][1000 genomes]
rs11003693	0.92[EUR][1000 genomes]
rs11003695	0.94[EUR][1000 genomes]
rs11003696	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11003697	0.93[EUR][1000 genomes]
rs11003699	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11003701	0.93[EUR][1000 genomes]
rs11003702	0.93[EUR][1000 genomes]
rs11003704	0.94[EUR][1000 genomes]
rs11003706	0.92[EUR][1000 genomes]
rs11003714	0.93[EUR][1000 genomes]
rs11003715	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11003723	0.97[EUR][1000 genomes]
rs11003725	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11003768	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11003769	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11003781	0.84[EUR][1000 genomes]
rs11492404	0.94[EUR][1000 genomes]
rs12256611	0.84[EUR][1000 genomes]
rs12355362	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12769841	0.92[EUR][1000 genomes]
rs12772474	0.94[EUR][1000 genomes]
rs12779744	0.93[EUR][1000 genomes]
rs1489832	0.94[EUR][1000 genomes]
rs16937596	0.94[EUR][1000 genomes]
rs16937607	0.97[EUR][1000 genomes]
rs16937609	0.92[EUR][1000 genomes]
rs17343	0.95[EUR][1000 genomes]
rs17344	0.94[EUR][1000 genomes]
rs17345	0.93[EUR][1000 genomes]
rs17346	0.97[EUR][1000 genomes]
rs34684767	0.93[EUR][1000 genomes]
rs351853	0.94[EUR][1000 genomes]
rs35895688	0.94[EUR][1000 genomes]
rs35946044	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35957518	0.97[EUR][1000 genomes]
rs36046455	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs370415	0.94[EUR][1000 genomes]
rs386402	0.94[EUR][1000 genomes]
rs56282513	0.94[EUR][1000 genomes]
rs61859175	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7083485	0.93[EUR][1000 genomes]
rs7092924	0.93[EUR][1000 genomes]
rs7093101	0.93[EUR][1000 genomes]
rs7098115	0.93[EUR][1000 genomes]
rs7098708	0.93[EUR][1000 genomes]
rs7100246	0.91[ASN][1000 genomes]
rs71490970	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767605	0.93[EUR][1000 genomes]
rs7898956	0.95[EUR][1000 genomes]
rs7900645	0.94[EUR][1000 genomes]
rs7903110	0.88[ASN][1000 genomes]
rs9733895	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752952	chr10:54900994-55497594	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1044282	chr10:55186501-55516392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv540631	chr10:55186501-55516392	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1043501	chr10:55186701-55516253	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv540632	chr10:55186701-55516253	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1050323	chr10:55190079-55546575	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2757386	chr10:55357136-55531037	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2759753	chr10:55357136-55586930	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2758220	chr10:55360612-55586930	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1047468	chr10:55361202-55459392	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv515498	chr10:55371601-55454152	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv1847684	chr10:55371601-55638740	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv8666	chr10:55371860-55459830	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1044236	chr10:55372005-55426888	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1040454	chr10:55372005-55457884	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv467208	chr10:55378668-55423964	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv550932	chr10:55378668-55423964	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv470941	chr10:55378668-55454151	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv3693056	chr10:55378668-55454152	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv438174	chr10:55378668-55454152	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv1842975	chr10:55378668-55736655	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1054744	chr10:55379719-55456587	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1051388	chr10:55379719-55457393	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv1053647	chr10:55379719-55457884	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1043179	chr10:55379719-55463942	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv2760118	chr10:55379731-55457896	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1035366	chr10:55380381-55457306	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv1046336	chr10:55380381-55457884	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv34540	chr10:55383168-55457394	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv34353	chr10:55383168-55479314	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv895410	chr10:55385962-55577022	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv895411	chr10:55390656-55417666	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
33	esv2755263	chr10:55394094-55546994	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
34	nsv550933	chr10:55395318-55405696	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv895412	chr10:55395380-55418087	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv895413	chr10:55395380-55446058	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv895414	chr10:55395380-55449214	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv895415	chr10:55395380-55473976	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv895416	chr10:55395380-55539954	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
40	nsv895417	chr10:55396233-55413116	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17696599	NCRNA00230B	trans	lymphoblastoid	seeQTL
rs17696599	LGALS12	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:55403200-55406200	Enhancers	Fetal Lung	lung
2	chr10:55405200-55407400	Enhancers	Fetal Stomach	stomach

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