Variant report

Variant	rs1454925
Chromosome Location	chr5:57336494-57336495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57334929..57336720-chr5:57754003..57756579,2	MCF-7	breast:
2	chr5:57316222..57318915-chr5:57334723..57336963,2	MCF-7	breast:
3	chr5:57321582..57323456-chr5:57334813..57337074,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10472030	0.84[ASN][1000 genomes]
rs11740997	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741208	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741819	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11742445	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11749915	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13160441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349957	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1352609	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1352610	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378248	0.82[EUR][1000 genomes]
rs1387641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454918	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454920	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454924	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1454928	0.82[AMR][1000 genomes]
rs1489791	0.87[AMR][1000 genomes]
rs1489797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17749982	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1826101	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844437	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699920	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700245	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56976559	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60707702	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61636750	0.85[AMR][1000 genomes]
rs62359093	0.85[AMR][1000 genomes]
rs62359098	0.85[AMR][1000 genomes]
rs62359144	0.80[AMR][1000 genomes]
rs62359145	0.80[AMR][1000 genomes]
rs62359146	0.87[AMR][1000 genomes]
rs62359148	0.87[AMR][1000 genomes]
rs62360186	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62360187	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62360200	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62368373	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368399	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62368400	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368401	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368402	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368405	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368406	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368407	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368408	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368409	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368410	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368411	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368412	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368413	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368414	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368415	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450458	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884729	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6886096	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7713227	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7736576	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs984926	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	esv1817904	chr5:57277522-57359476	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv1829717	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv1830976	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1837615	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1846984	chr5:57277522-57359476	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1850205	chr5:57277522-57359476	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv508357	chr5:57304472-57360187	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1015769	chr5:57309031-57338357	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv598229	chr5:57309072-57345166	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv4840	chr5:57311002-57352746	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv2763867	chr5:57314217-57360670	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3434910	chr5:57317244-57340175	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	esv3324417	chr5:57318244-57336897	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv1821795	chr5:57320343-57336494	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	nsv272	chr5:57320938-57339546	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	nsv1017266	chr5:57321586-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv1031966	chr5:57321586-57341144	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	nsv1033414	chr5:57321646-57338357	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv1023958	chr5:57321646-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	esv1796448	chr5:57323612-57338885	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	esv1803353	chr5:57323612-57338885	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	nsv1031755	chr5:57326015-57338357	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	nsv1018137	chr5:57326015-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
24	nsv1022023	chr5:57326015-57341014	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
25	nsv1031567	chr5:57326015-57341144	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
26	nsv1033110	chr5:57326015-57342120	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
27	esv1792664	chr5:57326015-57342152	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
28	nsv1020020	chr5:57326015-57342152	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
29	esv1827516	chr5:57326027-57341144	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
30	nsv1028094	chr5:57326151-57338357	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
31	nsv1034592	chr5:57326151-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
32	nsv1021126	chr5:57326151-57341144	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
33	nsv1026096	chr5:57326268-57338357	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
34	nsv598235	chr5:57326833-57340902	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
35	nsv598236	chr5:57326833-57343495	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
36	esv1827589	chr5:57326833-57345166	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
37	esv1846174	chr5:57326833-57345166	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
38	nsv1020073	chr5:57329103-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
39	nsv1024132	chr5:57329103-57341144	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
40	nsv1016751	chr5:57329518-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
41	nsv1019431	chr5:57329744-57340073	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
42	nsv1017677	chr5:57329744-57342152	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
43	nsv1023356	chr5:57329835-57341014	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
44	nsv1035077	chr5:57329835-57341144	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
45	nsv1023875	chr5:57329887-57341144	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1454925	SLC38A9	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57332600-57338200	Weak transcription	Stomach Mucosa	stomach
2	chr5:57335200-57339000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:57335800-57336800	Enhancers	HMEC	breast
4	chr5:57335800-57337000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:57335800-57337000	Enhancers	NHDF-Ad	bronchial
6	chr5:57335800-57337200	Enhancers	HSMM	muscle
7	chr5:57335800-57337400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:57336000-57336600	Enhancers	Osteobl	bone
9	chr5:57336000-57336800	Enhancers	NHEK	skin
10	chr5:57336000-57337000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:57336000-57337000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:57336000-57337000	Enhancers	Hela-S3	cervix
13	chr5:57336000-57337000	Enhancers	NH-A	brain
14	chr5:57336000-57337200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:57336000-57337200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:57336000-57337200	Weak transcription	K562	blood
17	chr5:57336200-57338800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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