Variant report

Variant	rs12239029
Chromosome Location	chr1:188847165-188847166
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:188846061..188848491-chr1:188851171..188853585,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10494620	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10920923	0.93[ASN][1000 genomes]
rs1445670	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445671	1.00[ASN][1000 genomes]
rs1445672	1.00[ASN][1000 genomes]
rs1445673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445674	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829499	1.00[ASN][1000 genomes]
rs16829521	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829525	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829527	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs16829528	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829531	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829532	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829534	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829536	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829539	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829542	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829562	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829563	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829637	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829642	0.93[ASN][1000 genomes]
rs16829647	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41468148	1.00[ASN][1000 genomes]
rs60025276	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6428035	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671266	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679894	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679901	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73050394	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73052403	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73057858	0.93[ASN][1000 genomes]
rs73068952	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068953	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068955	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068956	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068957	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068959	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068960	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068963	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068964	1.00[ASN][1000 genomes]
rs73068971	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068976	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068977	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068979	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138016	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74138017	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74138196	1.00[ASN][1000 genomes]
rs74140004	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427749	1.00[ASN][1000 genomes]
rs9804040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804108	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:44 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008537	chr1:188591251-188972682	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv997246	chr1:188609800-188961632	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535229	chr1:188609800-188961632	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872621	chr1:188647587-189128124	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv872622	chr1:188677169-188870483	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv470753	chr1:188683442-188850861	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2762410	chr1:188705757-189121717	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv872623	chr1:188711452-189128124	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv872624	chr1:188711452-189337997	Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1001827	chr1:188730015-189126074	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1006082	chr1:188730015-189163489	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv535230	chr1:188730015-189163489	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	esv2754486	chr1:188731343-189181343	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv466417	chr1:188735336-188870483	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv548475	chr1:188735336-188870483	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv872625	chr1:188746396-188870483	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv548476	chr1:188750901-188850861	Active TSS Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv548477	chr1:188750901-188870483	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv872626	chr1:188750901-189343623	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv466428	chr1:188760628-188870483	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv548478	chr1:188760628-188870483	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv466439	chr1:188764543-188870483	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv548479	chr1:188764543-188870483	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv872627	chr1:188764543-189188538	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv872628	chr1:188764543-189211622	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	nsv466450	chr1:188770589-188883037	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv548480	chr1:188770589-188883037	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv872629	chr1:188770589-189117170	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
29	nsv872630	chr1:188773111-189128124	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
30	nsv872631	chr1:188773111-189282802	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
31	nsv1005282	chr1:188773549-189191697	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
32	nsv535231	chr1:188773549-189191697	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
33	nsv548481	chr1:188787390-188888360	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
34	nsv466461	chr1:188802542-188931828	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
35	nsv548482	chr1:188802542-188931828	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
36	nsv872632	chr1:188802542-188931828	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
37	nsv872633	chr1:188802542-189147056	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
38	nsv548483	chr1:188802542-189672228	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
39	nsv872634	chr1:188806530-188862962	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
40	nsv872635	chr1:188813880-188870483	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
41	nsv872636	chr1:188822394-188883037	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
42	nsv1001114	chr1:188835200-188961632	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
43	nsv947457	chr1:188837500-188864451	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
44	nsv1002943	chr1:188839762-189125021	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:188846600-188847200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:188846600-188847600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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