Variant report

Variant	rs13015010
Chromosome Location	chr2:40195548-40195549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1013954	0.92[ASN][1000 genomes]
rs10181331	0.87[ASN][1000 genomes]
rs10191782	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10194236	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10194406	0.81[AMR][1000 genomes]
rs10200630	0.86[ASN][1000 genomes]
rs10490338	0.87[ASN][1000 genomes]
rs10779927	0.89[ASN][1000 genomes]
rs10779928	0.82[ASN][1000 genomes]
rs10865160	0.86[ASN][1000 genomes]
rs10865162	0.82[ASN][1000 genomes]
rs11124713	0.96[ASN][1000 genomes]
rs11124723	0.91[ASN][1000 genomes]
rs11124724	0.81[ASN][1000 genomes]
rs11124726	0.83[ASN][1000 genomes]
rs11124727	0.84[ASN][1000 genomes]
rs11685420	0.96[ASN][1000 genomes]
rs11888334	0.88[ASN][1000 genomes]
rs11889689	0.88[ASN][1000 genomes]
rs11893312	0.88[ASN][1000 genomes]
rs11902593	0.88[ASN][1000 genomes]
rs12463415	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12474732	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622032	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712668	0.88[ASN][1000 genomes]
rs12712669	0.88[ASN][1000 genomes]
rs12988439	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13015269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390026	0.89[ASN][1000 genomes]
rs1476989	0.86[ASN][1000 genomes]
rs1476990	0.83[ASN][1000 genomes]
rs1541561	0.84[ASN][1000 genomes]
rs1548876	0.93[ASN][1000 genomes]
rs17024711	0.92[ASN][1000 genomes]
rs17024746	0.89[ASN][1000 genomes]
rs17024767	0.81[ASN][1000 genomes]
rs17024801	0.85[ASN][1000 genomes]
rs17024804	0.85[ASN][1000 genomes]
rs17024807	0.85[ASN][1000 genomes]
rs17024825	0.84[ASN][1000 genomes]
rs17024827	0.84[ASN][1000 genomes]
rs17024830	0.84[ASN][1000 genomes]
rs17024833	0.84[ASN][1000 genomes]
rs1861250	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1861251	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2058636	0.86[ASN][1000 genomes]
rs2058637	0.86[ASN][1000 genomes]
rs2058638	0.87[ASN][1000 genomes]
rs2058639	0.85[ASN][1000 genomes]
rs2080298	0.88[ASN][1000 genomes]
rs2215967	0.91[ASN][1000 genomes]
rs2215974	0.81[ASN][1000 genomes]
rs2373705	0.84[ASN][1000 genomes]
rs2373708	0.88[ASN][1000 genomes]
rs2373709	0.88[ASN][1000 genomes]
rs2373710	0.94[ASN][1000 genomes]
rs28649544	0.83[ASN][1000 genomes]
rs2888639	0.88[ASN][1000 genomes]
rs4321345	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519500	0.93[ASN][1000 genomes]
rs4538248	0.85[ASN][1000 genomes]
rs56118530	0.84[ASN][1000 genomes]
rs57677588	0.93[ASN][1000 genomes]
rs58224754	0.84[ASN][1000 genomes]
rs58570175	0.83[ASN][1000 genomes]
rs58969983	0.84[ASN][1000 genomes]
rs59034193	0.84[ASN][1000 genomes]
rs59073176	0.84[ASN][1000 genomes]
rs59110768	0.88[ASN][1000 genomes]
rs59957738	0.83[ASN][1000 genomes]
rs60613668	0.83[ASN][1000 genomes]
rs61481161	0.90[ASN][1000 genomes]
rs61604673	0.89[ASN][1000 genomes]
rs62136383	0.96[ASN][1000 genomes]
rs62137255	0.86[ASN][1000 genomes]
rs62150227	0.92[ASN][1000 genomes]
rs62150228	0.92[ASN][1000 genomes]
rs62150232	0.88[ASN][1000 genomes]
rs62150235	0.88[ASN][1000 genomes]
rs62151493	0.84[ASN][1000 genomes]
rs62151494	0.86[ASN][1000 genomes]
rs62151495	0.84[ASN][1000 genomes]
rs62151497	0.82[ASN][1000 genomes]
rs6544273	0.83[ASN][1000 genomes]
rs6544274	0.88[ASN][1000 genomes]
rs6544275	0.87[ASN][1000 genomes]
rs6544277	0.87[ASN][1000 genomes]
rs6544280	0.92[ASN][1000 genomes]
rs6544282	0.92[ASN][1000 genomes]
rs6544296	0.90[ASN][1000 genomes]
rs6725817	0.80[ASN][1000 genomes]
rs6735955	0.80[ASN][1000 genomes]
rs72940717	0.84[ASN][1000 genomes]
rs741270	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557819	0.83[ASN][1000 genomes]
rs7558203	0.82[ASN][1000 genomes]
rs7564200	0.84[ASN][1000 genomes]
rs7564447	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572755	0.98[ASN][1000 genomes]
rs7584288	0.87[ASN][1000 genomes]
rs7590992	0.84[ASN][1000 genomes]
rs7591069	0.84[ASN][1000 genomes]
rs7591263	0.84[ASN][1000 genomes]
rs759353	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs759356	0.90[ASN][1000 genomes]
rs759357	0.89[ASN][1000 genomes]
rs759358	0.82[ASN][1000 genomes]
rs7599493	0.90[ASN][1000 genomes]
rs7600580	0.93[ASN][1000 genomes]
rs7607156	0.89[ASN][1000 genomes]
rs7607499	0.89[ASN][1000 genomes]
rs768271	0.96[ASN][1000 genomes]
rs8179517	0.89[ASN][1000 genomes]
rs917970	0.93[ASN][1000 genomes]
rs917971	0.92[ASN][1000 genomes]
rs917974	0.91[ASN][1000 genomes]
rs957117	0.99[ASN][1000 genomes]
rs9749783	0.91[ASN][1000 genomes]
rs979716	0.80[ASN][1000 genomes]
rs985455	0.99[ASN][1000 genomes]
rs9973551	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010609	chr2:40107234-40231674	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv535652	chr2:40107234-40231674	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873893	chr2:40137942-40222206	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873894	chr2:40139250-40198380	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv873895	chr2:40139250-40207338	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873896	chr2:40139250-40208665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873897	chr2:40139250-40225253	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv869668	chr2:40141079-40249854	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1003920	chr2:40141776-40245464	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1000423	chr2:40143646-40245464	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv456385	chr2:40151882-40195548	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv581497	chr2:40151882-40195548	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv456396	chr2:40154844-40231282	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv581498	chr2:40154844-40231282	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv581499	chr2:40154844-40241868	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv873898	chr2:40156882-40246716	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv456407	chr2:40158363-40208665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv581500	chr2:40158363-40208665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv873899	chr2:40161168-40281964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1006550	chr2:40164769-40209936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
23	nsv1009532	chr2:40165606-40291224	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv535653	chr2:40165606-40291224	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13015010	SLC8A1-AS1	cis	Esophagus Mucosa	GTEx
rs13015010	SRSF7	cis	parietal	SCAN
rs13015010	DHX57	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40182000-40218000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40194000-40196400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:40195400-40199200	Weak transcription	HSMM	muscle

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