Variant report

Variant	rs10499338
Chromosome Location	chr7:3522403-3522404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:3521696..3522495-chr7:3631928..3632648,2	MCF-7	breast:
2	chr7:3439202..3440208-chr7:3521793..3522518,3	MCF-7	breast:
3	chr7:3521755..3523053-chr7:3688631..3689551,7	MCF-7	breast:
4	chr7:3521823..3522640-chr7:3807742..3808264,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10215554	0.81[JPT][hapmap]
rs10216009	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs10227151	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs10238783	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs10272876	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10275747	0.85[CEU][hapmap]
rs10277776	0.80[JPT][hapmap]
rs10499336	0.80[CEU][hapmap]
rs10499337	0.80[CEU][hapmap]
rs1108879	0.85[CHB][hapmap]
rs1114778	0.81[ASN][1000 genomes]
rs11531491	0.87[ASN][1000 genomes]
rs12111969	1.00[CHB][hapmap]
rs12672248	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[MEX][hapmap]
rs1403161	0.81[ASN][1000 genomes]
rs1522505	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs1548209	0.83[CHB][hapmap]
rs1608136	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[MEX][hapmap]
rs16870870	0.83[ASN][1000 genomes]
rs17133420	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs17133426	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs17133432	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17133439	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs17133442	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17133445	0.88[ASN][1000 genomes]
rs17133501	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap]
rs17133520	1.00[CHB][hapmap]
rs17133523	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs17133555	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1882429	0.83[CHB][hapmap]
rs1922017	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap]
rs1922019	1.00[CHB][hapmap]
rs2141819	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141821	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2177168	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2177169	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2178626	0.81[JPT][hapmap]
rs2272526	1.00[CHB][hapmap]
rs2272527	1.00[CHB][hapmap]
rs35791987	0.81[ASN][1000 genomes]
rs4273759	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4291167	0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs4496870	0.95[CHB][hapmap]
rs55643551	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56234403	0.81[ASN][1000 genomes]
rs57733415	0.90[ASN][1000 genomes]
rs58748813	0.82[ASN][1000 genomes]
rs58979693	0.93[ASN][1000 genomes]
rs60268542	0.81[ASN][1000 genomes]
rs6462121	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67955951	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs68143552	0.81[ASN][1000 genomes]
rs6947615	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap]
rs6966652	0.81[AMR][1000 genomes]
rs73035954	0.80[ASN][1000 genomes]
rs73038556	0.99[ASN][1000 genomes]
rs73671854	0.89[ASN][1000 genomes]
rs7780639	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7787559	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7794763	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs7795323	1.00[CHB][hapmap]
rs7800962	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7805598	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap]
rs9654994	0.81[JPT][hapmap]
rs9771445	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020764	chr7:3348458-3554820	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv538662	chr7:3348458-3554820	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2764026	chr7:3365002-3618361	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1015296	chr7:3381813-3560401	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv528715	chr7:3451251-3598581	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv605902	chr7:3464896-3598581	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv605903	chr7:3472721-3527925	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv887333	chr7:3475716-3542488	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv869723	chr7:3482682-3566293	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv464270	chr7:3490865-3581357	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv605904	chr7:3490865-3581357	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1027426	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv538672	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1034716	chr7:3512406-3616155	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv1801470	chr7:3521000-3541046	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1030469	chr7:3521036-3554820	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv538673	chr7:3521036-3554820	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10499338	SDK1	cis	parietal	SCAN
rs10499338	NENF	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3491200-3526600	Weak transcription	Pancreas	Pancrea
2	chr7:3521400-3528400	Weak transcription	Aorta	Aorta
3	chr7:3522000-3522600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr7:3522000-3522600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr7:3522000-3522600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:3522000-3522600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr7:3522000-3522600	Enhancers	HepG2	liver
8	chr7:3522200-3522600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr7:3522200-3522600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr7:3522200-3522600	Enhancers	A549	lung
11	chr7:3522200-3523400	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr7:3522400-3522600	Enhancers	H9 Cell Line	embryonic stem cell

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