Variant report

Variant	rs1352610
Chromosome Location	chr5:57321586-57321587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57321582..57323456-chr5:57334813..57337074,3	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10472030	0.84[ASN][1000 genomes]
rs11740997	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741208	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741819	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11742445	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11749915	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13160441	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349957	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1352609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378248	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1387641	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454918	0.92[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1454920	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454924	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454925	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454926	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1454928	0.85[AMR][1000 genomes]
rs1489791	0.91[AMR][1000 genomes]
rs1489797	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17749982	0.81[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1826101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826106	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699920	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700243	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700244	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700245	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56976559	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60707702	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61636750	0.89[AMR][1000 genomes]
rs62359093	0.89[AMR][1000 genomes]
rs62359098	0.89[AMR][1000 genomes]
rs62359144	0.84[AMR][1000 genomes]
rs62359145	0.84[AMR][1000 genomes]
rs62359146	0.91[AMR][1000 genomes]
rs62359148	0.91[AMR][1000 genomes]
rs62360185	0.83[AMR][1000 genomes]
rs62360186	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62360187	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62360200	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62368373	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368399	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62368400	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368401	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368402	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368406	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368407	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368408	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368409	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62368410	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368411	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368412	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368413	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368414	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62368415	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450458	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884729	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6886096	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7713227	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7736576	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs984926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 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	nsv1020936	chr5:57309031-57333521	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv1015769	chr5:57309031-57338357	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv598229	chr5:57309072-57345166	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1018119	chr5:57309406-57332632	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
12	nsv1019152	chr5:57310368-57332632	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
13	nsv1016557	chr5:57310368-57332943	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
14	nsv1021803	chr5:57310368-57333521	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
15	nsv4840	chr5:57311002-57352746	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv1804295	chr5:57312154-57333508	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
17	esv1808533	chr5:57312154-57333508	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
18	nsv1022237	chr5:57313235-57332542	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv1023759	chr5:57314205-57333521	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	esv2763867	chr5:57314217-57360670	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv3434910	chr5:57317244-57340175	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	esv3324417	chr5:57318244-57336897	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	nsv1027930	chr5:57319482-57332385	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv1032117	chr5:57319482-57332632	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
25	nsv1017741	chr5:57319482-57333521	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
26	esv1821795	chr5:57320343-57336494	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
27	nsv272	chr5:57320938-57339546	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
28	esv3468460	chr5:57321495-57335693	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
29	nsv1026050	chr5:57321586-57332319	Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
30	nsv1017591	chr5:57321586-57332542	Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
31	nsv1019312	chr5:57321586-57332943	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
32	nsv1026453	chr5:57321586-57333281	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
33	nsv1030919	chr5:57321586-57333521	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
34	nsv1017266	chr5:57321586-57340073	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
35	nsv1031966	chr5:57321586-57341144	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1352610	SLC38A9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57321400-57321600	Enhancers	Right Ventricle	heart

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