Variant report

Variant	rs17659389
Chromosome Location	chr1:152539393-152539394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:152539253-152539483	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:152539283-152539721	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:152539192-152539605	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:152539232-152539597	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:152539193-152539608	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:152539172-152539644	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:152539226-152539601	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:152539255-152539540	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr1:152539282-152539594	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
LCE3E	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10788847	1.00[CHB][hapmap]
rs11205040	1.00[YRI][hapmap]
rs11205064	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs11205086	1.00[CHB][hapmap]
rs11585409	1.00[CHB][hapmap]
rs12728274	1.00[CHB][hapmap]
rs12733893	1.00[CHB][hapmap]
rs12754243	1.00[CHB][hapmap]
rs12754873	1.00[CHB][hapmap]
rs1412541	1.00[CHB][hapmap]
rs57201979	0.84[AFR][1000 genomes]
rs59861223	0.84[AFR][1000 genomes]
rs73005820	0.84[AFR][1000 genomes]
rs7550666	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:71 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2750810	chr1:152453669-152660927	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv1798404	chr1:152472839-152587113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1827111	chr1:152472839-152690073	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv1830764	chr1:152472839-152690073	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv547860	chr1:152497685-152553365	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv547861	chr1:152508562-152553365	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv547862	chr1:152508562-152591142	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv463861	chr1:152510348-152553365	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv547863	chr1:152510348-152553365	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1001597	chr1:152511269-152555134	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv535162	chr1:152511269-152555134	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv463872	chr1:152514332-152553365	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv547864	chr1:152514332-152553365	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1000403	chr1:152517845-152556402	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv1000036	chr1:152519124-152555134	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv999353	chr1:152526643-152555176	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
20	nsv1003895	chr1:152526643-152555515	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
21	nsv1008009	chr1:152526643-152556402	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
22	nsv1002425	chr1:152526643-152586582	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	esv2762965	chr1:152526643-152586594	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv547865	chr1:152526812-152553365	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
25	nsv547866	chr1:152526812-152555005	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
26	nsv547867	chr1:152526812-152561408	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
27	nsv998381	chr1:152528295-152555134	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
28	nsv535163	chr1:152528295-152555134	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
29	nsv1014078	chr1:152528295-152572936	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
30	nsv535164	chr1:152528295-152572936	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
31	nsv535165	chr1:152528295-152591912	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
32	nsv463883	chr1:152529832-152550018	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
33	nsv547868	chr1:152529832-152550018	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
34	nsv463894	chr1:152529832-152553365	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
35	nsv463905	chr1:152529832-152553365	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
36	nsv463916	chr1:152529832-152553365	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
37	nsv463927	chr1:152529832-152553365	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
38	nsv463938	chr1:152529832-152553365	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
39	nsv463951	chr1:152529832-152553365	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
40	nsv463962	chr1:152529832-152553365	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
41	nsv463973	chr1:152529832-152553365	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
42	nsv547869	chr1:152529832-152553365	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
43	nsv547870	chr1:152529832-152590565	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
44	nsv463984	chr1:152529832-152591142	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
45	nsv547871	chr1:152529832-152591142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
46	nsv547872	chr1:152530510-152549876	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
47	nsv547873	chr1:152530510-152550018	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
48	nsv547874	chr1:152530510-152551276	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
49	nsv516961	chr1:152530510-152553365	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
50	nsv470739	chr1:152530510-152553365	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17659389	AQP10	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152538400-152539600	Enhancers	HMEC	breast
2	chr1:152538400-152539800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152538800-152539400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152538800-152539800	Enhancers	NHEK	skin
5	chr1:152539000-152539600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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