Variant report

Variant	rs13042179
Chromosome Location	chr20:14397951-14397952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:14392722..14394222-chr20:14395947..14398400,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs13036742	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13036861	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13036915	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13037096	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13038046	1.00[CEU][hapmap]
rs13038084	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13039188	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13039594	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13039619	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13039855	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13039862	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13040337	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13040558	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13040987	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13041262	0.89[CEU][hapmap]
rs13041600	1.00[CEU][hapmap]
rs13042866	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13043921	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13044705	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13044911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13045655	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17226957	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17226971	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17226999	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17812658	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17812676	1.00[CEU][hapmap]
rs1998236	0.90[CEU][hapmap]
rs2210655	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34021592	0.81[EUR][1000 genomes]
rs34085437	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34094793	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34287609	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34522477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34538736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34671733	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34824714	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34880844	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34896694	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34955232	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34985688	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35171263	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35346025	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35438476	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35445955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35505382	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35511588	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35554517	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35577212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35610301	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35631624	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35649042	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35733982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35747430	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35760794	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35763852	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35943017	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35989081	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36062805	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36134325	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41328645	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4630827	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4814301	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs62204373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62204396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62204398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62204402	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62204403	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62204406	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62204411	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62204429	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62204435	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62204437	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62207626	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62207627	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62207628	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs74179739	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74179740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74179742	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs915074	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs915075	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs963329	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1061705	chr20:14330029-14430604	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1062079	chr20:14334350-14429820	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1063787	chr20:14341199-14408090	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv585440	chr20:14352394-14457834	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1063733	chr20:14357857-14459453	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv585441	chr20:14374573-14455497	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1064721	chr20:14384931-14648223	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14393800-14398600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr20:14394400-14398600	Enhancers	Fetal Intestine Small	intestine
3	chr20:14395600-14403400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr20:14396200-14399400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr20:14396400-14398800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:14396400-14399000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:14396400-14403400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr20:14396600-14398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr20:14396600-14398800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:14396600-14399000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr20:14397600-14403600	Weak transcription	Fetal Intestine Large	intestine

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