Variant report

Variant	rs9654994
Chromosome Location	chr7:3617414-3617415
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	chr7:3609002..3610756-chr7:3616407..3619133,2	MCF-7	breast:

Extended variants
information (count: 207 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10215541	0.90[ASN][1000 genomes]
rs10215554	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs10215632	0.93[ASN][1000 genomes]
rs10216009	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs10227151	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs10233162	0.80[JPT][hapmap]
rs10236989	0.91[ASN][1000 genomes]
rs10238142	0.80[ASN][1000 genomes]
rs10238783	0.90[JPT][hapmap]
rs10241070	0.91[ASN][1000 genomes]
rs10243981	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs10260558	0.82[ASN][1000 genomes]
rs10263338	0.83[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs10263702	0.80[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10264275	0.90[ASN][1000 genomes]
rs10272876	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs10276626	0.80[JPT][hapmap]
rs10277776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10499338	0.81[JPT][hapmap]
rs10951254	0.86[CHD][hapmap]
rs11531493	0.90[ASN][1000 genomes]
rs11767639	0.86[CHD][hapmap]
rs11979940	0.80[ASN][1000 genomes]
rs12055947	0.82[JPT][hapmap]
rs12111969	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12670592	0.91[ASN][1000 genomes]
rs12672248	0.95[JPT][hapmap]
rs1522505	0.90[JPT][hapmap]
rs1608136	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs16870900	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17133420	0.95[JPT][hapmap]
rs17133426	0.95[JPT][hapmap]
rs17133432	0.95[JPT][hapmap]
rs17133501	0.90[JPT][hapmap]
rs17133520	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs17133523	0.82[ASW][hapmap];0.95[JPT][hapmap]
rs17133533	0.85[ASN][1000 genomes]
rs17133535	0.88[ASN][1000 genomes]
rs17133554	0.90[ASN][1000 genomes]
rs17133555	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17133566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17133591	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1864842	0.81[CHD][hapmap]
rs1882429	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1922014	0.83[ASN][1000 genomes]
rs1922015	0.84[ASN][1000 genomes]
rs1922017	0.95[JPT][hapmap];0.83[YRI][hapmap]
rs1922019	0.95[JPT][hapmap]
rs1991758	0.84[ASN][1000 genomes]
rs2016197	0.85[ASN][1000 genomes]
rs2060179	0.81[ASN][1000 genomes]
rs2141819	0.90[JPT][hapmap]
rs2141821	0.90[JPT][hapmap]
rs2141825	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177168	0.90[JPT][hapmap]
rs2178626	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272526	0.94[JPT][hapmap]
rs2272527	0.95[JPT][hapmap]
rs2341578	0.81[CHD][hapmap]
rs2341587	0.84[CHD][hapmap]
rs2614966	0.81[JPT][hapmap]
rs2705606	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs28412607	0.90[ASN][1000 genomes]
rs28451147	0.91[ASN][1000 genomes]
rs28832366	0.90[ASN][1000 genomes]
rs3817615	0.85[CHD][hapmap]
rs4291167	0.89[JPT][hapmap]
rs4496870	0.90[JPT][hapmap]
rs4722952	0.83[CHB][hapmap]
rs56329315	0.85[ASN][1000 genomes]
rs56669571	0.85[ASN][1000 genomes]
rs56995955	0.88[ASN][1000 genomes]
rs57125879	0.84[ASN][1000 genomes]
rs57462209	0.93[ASN][1000 genomes]
rs57473088	0.84[ASN][1000 genomes]
rs57480717	0.85[ASN][1000 genomes]
rs58498999	0.88[ASN][1000 genomes]
rs59465686	0.87[ASN][1000 genomes]
rs60372133	0.84[ASN][1000 genomes]
rs61425932	0.85[ASN][1000 genomes]
rs6462121	0.90[JPT][hapmap]
rs6462200	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs6947615	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6959706	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6961261	0.85[ASN][1000 genomes]
rs6964347	0.88[CHD][hapmap]
rs6966652	0.88[ASN][1000 genomes]
rs6971989	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs73673633	0.85[ASN][1000 genomes]
rs73673634	0.85[ASN][1000 genomes]
rs7782934	0.84[ASN][1000 genomes]
rs7787559	0.94[JPT][hapmap]
rs7795323	0.95[JPT][hapmap]
rs7800962	0.90[JPT][hapmap]
rs7802868	0.88[ASN][1000 genomes]
rs7805598	0.90[JPT][hapmap]
rs7807210	0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs957360	0.83[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9638859	0.81[ASN][1000 genomes]
rs9771445	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:107 , 50 per page) page: 1 2 3

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	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
4	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
5	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
6	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
7	nsv887334	chr7:3531275-3635105	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1023888	chr7:3539750-3638242	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1034298	chr7:3539750-3646251	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1029264	chr7:3549193-3622532	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv1840932	chr7:3585560-3618827	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv1792280	chr7:3592290-3668229	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1022135	chr7:3601840-3618349	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv2757205	chr7:3602348-3630349	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv2759501	chr7:3602348-3630349	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1017012	chr7:3602397-3638242	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv538679	chr7:3602397-3638242	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv605909	chr7:3605340-3638547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1028640	chr7:3606640-3617998	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1025521	chr7:3606640-3618349	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv1838607	chr7:3606640-3618361	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv2752641	chr7:3609495-3631115	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	esv1835418	chr7:3609712-3618143	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv517279	chr7:3609712-3618143	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv818474	chr7:3609712-3618143	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv2752926	chr7:3609712-3631115	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv2754251	chr7:3609712-3631115	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv605910	chr7:3609821-3618143	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv1835447	chr7:3609821-3618361	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv1017452	chr7:3609821-3624792	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv1016783	chr7:3609821-3624853	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv1030806	chr7:3609821-3625238	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv1022755	chr7:3609821-3626615	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv1015396	chr7:3609821-3626689	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv948390	chr7:3609821-3734421	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
37	esv1838067	chr7:3609843-3618361	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
38	esv1838414	chr7:3609843-3618361	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv442026	chr7:3609843-3618361	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
40	esv1812450	chr7:3609982-3617808	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
41	esv1795945	chr7:3610182-3617608	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
42	esv1806284	chr7:3610182-3617608	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
43	esv1819441	chr7:3610182-3617608	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
44	esv1829974	chr7:3610182-3617608	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
45	esv1850048	chr7:3610182-3617608	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
46	nsv8032	chr7:3610210-3622374	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
47	esv3477091	chr7:3610272-3619100	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
48	esv1837452	chr7:3610303-3618349	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
49	esv1838367	chr7:3610303-3618349	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
50	esv1834400	chr7:3610303-3618361	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9654994	PRKAR1B	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3613200-3625200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:3616600-3617600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:3617000-3619200	Weak transcription	Stomach Mucosa	stomach
4	chr7:3617200-3620400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:3617200-3622600	Weak transcription	Pancreas	Pancrea
6	chr7:3617400-3618200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:3617400-3622600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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